Maybe consider specifying a command to run at initial connection to set your RDi job's library list.
We use a custom program to make it easy to set "commonly used" library lists.
To start: I right-click one of my connections, then select "Properties",
On the "Properties for xxx" window, on the Left, select "Subsystems"
From the " Subsystems" pane to the Right, in "Initial command:" I specify something like:
CALL PGM(liba/setlibl) PARM('xx' ' ')
For us "liba/setlibl" is a custom CL which uses the first, two character parm to select a library list and
current library from a local file and then do a CHGLIBL.
The second one character parm is a return parm that is ignored
CL source included below in case anyone is interested.
HTH 
CL source:
             PGM        PARM(&CMPFIL &RTNCDE)                           
                                                                        
             DCLF       FILE(XXINITL2)                                  
                                                                        
             DCL        VAR(&CMPFIL) TYPE(*CHAR) LEN(2) /* Input  +     
                          company file group */                         
             DCL        VAR(&DIVNBRP) TYPE(*CHAR) LEN(2) /* Division +  
                          number - parameter */                         
             DCL        VAR(&APLENVIRNP) TYPE(*CHAR) LEN(1) /* +        
                          Application environment - parameter */        
             DCL        VAR(&RTNCDE) TYPE(*CHAR) LEN(4) /* Return +     
                          code - parameter */                           
             DCL        VAR(&LIBL) TYPE(*CHAR) LEN(275) /* Library +    
                          list */                                       
             DCL        VAR(&CMD) TYPE(*CHAR) LEN(500) /* Command +     
                          string */                                     
             DCL        VAR(&MSGID) TYPE(*CHAR) LEN(7) /* Message +     
                          identifier */                                 
             DCL        VAR(&MSG) TYPE(*CHAR) LEN(79)                   
                                                                        
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
/*  Global monitor message.  If error received, go to error routine. */ 
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
                                                                        
             MONMSG     MSGID(CPF0000) EXEC(GOTO CMDLBL(ERROR))         
                                                                        
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
/*  Initialize the program return code to blank.                     */ 
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
                                                                        
             CHGVAR     VAR(&RTNCDE) VALUE('    ')                      
/*           IF         COND(&CMPFIL *EQ '  ') THEN(DO)  +              
             CHGVAR     VAR(&CMPFIL) VALUE('S1')         +              
             ENDDO                                       +              
             END     */                                                 
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
/* Position/read the XXINITL file to get the record for the division */ 
/*    number and application environment requested.                  */ 
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
                                                                        
 READ_FILE:  OVRDBF     FILE(XXINITL2) POSITION(*KEY 1 *N &CMPFIL)      
             RCVF                                                       
                                                                        
             IF         COND(&CMPFIL *NE &COMFIL) THEN(GOTO +           
                          CMDLBL(ERROR))                                
                                                                        
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
/*  Change the library list and current library using the library    */ 
/*    list library names for the division and application            */ 
/*    environment requested.                                         */ 
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
                                                                        
             CHGVAR     VAR(&LIBL) VALUE(&LIBLLIB01 *BCAT &LIBLLIB02 +  
                          *BCAT &LIBLLIB03 *BCAT &LIBLLIB04 *BCAT +     
                          &LIBLLIB05 *BCAT &LIBLLIB06 *BCAT +           
                          &LIBLLIB07 *BCAT &LIBLLIB08 *BCAT +           
                          &LIBLLIB09 *BCAT &LIBLLIB10 *BCAT +           
                          &LIBLLIB11 *BCAT &LIBLLIB12 *BCAT +           
                          &LIBLLIB13 *BCAT &LIBLLIB14 *BCAT +           
                          &LIBLLIB15 *BCAT &LIBLLIB16 *BCAT +           
                          &LIBLLIB17 *BCAT &LIBLLIB18 *BCAT +           
                          &LIBLLIB19 *BCAT &LIBLLIB20 *BCAT +           
                          &LIBLLIB21 *BCAT &LIBLLIB22 *BCAT +           
                          &LIBLLIB23 *BCAT &LIBLLIB24 *BCAT +           
                          &LIBLLIB25) /* Form library list */           
                                                                        
             IF         COND(&CURLIB *EQ '          ') THEN(CHGVAR +    
                          VAR(&CURLIB) VALUE('*CRTDFT   '))             
             CHGVAR     VAR(&CMD) VALUE('CHGLIBL LIBL(' *CAT &LIBL +    
                          *TCAT ') CURLIB(' *CAT &CURLIB *TCAT ')')     
             CALL       PGM(QCMDEXC) PARM(&CMD 500) /* Change +         
                          library list and current library */           
/*           IF         COND(&CMPFIL *EQ 'S1') THEN(DO)     +           
             CHGVAR     VAR(&CMPFIL) VALUE('  ')            +           
             ENDDO                                          +           
             END       */                                               
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
/*  Initialize the program return code to good.  Go to exit.         */ 
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
                                                                        
             CHGVAR     VAR(&RTNCDE) VALUE('GOOD')                      
             GOTO       CMDLBL(EXIT)                                    
                                                                        
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
/*  Error routine.  Set return code equal to the last four bytes of  */ 
/*    the message identifier.                                        */ 
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
                                                                        
 ERROR:      RCVMSG     MSGTYPE(*EXCP) RMV(*NO) MSGID(&MSGID)           
             CHGVAR     VAR(&RTNCDE) VALUE(%SST(&MSGID 4 4))            
             CHGVAR     VAR(&MSG) VALUE('* LIBL LIST NOT CHANGED. +     
                          INVALID FILE GROUP.')                         
             SNDPGMMSG  MSG(&MSG) TOPGMQ(*PRV)                          
             MONMSG     MSGID(CPF0000)                                  
                                                                        
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
/*  End of program.                                                  */ 
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ 
                                                                        
 EXIT:       RETURN                                                     
             ENDPGM                                                     
-----Original Message-----
From: WDSCI-L [mailto:wdsci-l-bounces@xxxxxxxxxxxx] On Behalf Of Vernon Hamberg
Sent: Tuesday, August 18, 2015 9:57 AM
To: Rational Developer for IBM i / Websphere Development Studio Client for System i & iSeries
Subject: Re: [WDSCI-L] How can I remove a library from a library filter?
Good point, Kurt
Many kinds of filters -
1. Library list filter - all you can do is give it a name, its contents are your *LIBL
   - You can remove libraries from the library list here, and add to the library list 2. Library filter - these CAN specify *LIBL or *ALLUSR or *USRLIBL - the various special values for any library parameter of a command, as well as (and in addition?) a list of individual libraries
   - You can add items here to your library list (items not already on the library list, right?)
   - You cannot remove anything from your library list here - only from a library list filter
Random thought - maybe you can use an object filter with *LIB as the 
object type - no idea - and why would you?   :)
HTH
Vern
On 8/18/2015 10:17 AM, Kurt Anderson wrote:
A temporary solution is to right-click the library and select "Remove From Library List."  That will only apply to the active connection.  Once you disconnect and reconnect (or close and re-open RDi), the library will be back.
To my knowledge you can't "Change" a library list filter.  It's grayed out for me.
I have a couple connections setup with a specific JOBD so the library list is as I want it (mostly) for those connections.  I'm not sure if that's a path you can take or not.  Having connections is also nice so when I do modify a library list on one connection via the filter, it's not also affecting other connections.
Kurt Anderson
Sr. Programmer/Analyst - Application Development, Service Delivery 
Platform
-----Original Message-----
From: WDSCI-L [mailto:wdsci-l-bounces@xxxxxxxxxxxx] On Behalf Of Jeff 
Young
Sent: Monday, August 17, 2015 4:06 PM
To: Rational Developer for IBM i / Websphere Development Studio Client 
for System i & iSeries <wdsci-l@xxxxxxxxxxxx>
Subject: Re: [WDSCI-L] How can I remove a library from a library filter?
What type of filter is it?
You should be able to right click on the filter name and select Change.
You will see a list on the left of all items in your filter.  You can remove an item from the filter by Left click/delete.
this removes it from the filter only, not the system.
Jeff Young
Sr. Programmer Analyst
On Mon, Aug 17, 2015 at 4:00 PM, DFreinkel 
<dfreinkel@xxxxxxxxxxxxxxxxx>
wrote:
I have several libraries in my one filter and need to remove the 
unwanted ones from the filter and not the system.
I cannot find a way to accomplish this.
Using the delete option physically removes the library.
TIA.
Darryl Freinkel.
Sent from my iPad
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