You can retrieve the source for the GO SAVE option 21: RTVCLSRC for pgm QMNSAVE and modify the commands used there to save the LINK (IFS) info, compile the program and run that iso the GO SAVE 21 option.Check this article http://www.itjungle.com/tfh/tfh082602-story04.html

This is possible without modifying QMNSAVE.  I will try to check before leaving work today and post back here. 
Strong recommend not modifying IBM’s program.

Found it.  Check out the info at item 2. below.  These instructions are from a V5R3 manual.  I don’t know if they apply to earlier releases but would be surprised if they do not since virutual optical images have been around for a while.
Attention: If you are using the Hardware Management Console for eServer™ (HMC), you must back up the HMC in addition to using the GO SAVE: Option 21 to obtain a complete save of your system. See Backing up your HMC for details on saving your HMC.

Sign on with a user profile that has *SAVSYS and *JOBCTL special authorities, and also has sufficient authority to list different types of server resources. (The QSECOFR user profile contains all of these authorities.) This ensures that you have the authority that you need to place the server in the necessary state and to save everything.
Virtual optical images can significantly increase the time it takes to complete an Option 21 save operation, even if the image catalog entries do not contain data. If you want to exclude virtual images from a full system save, use one of the following strategies:

Use the Change Attribute (CHGATR) command to mark the image catalog directory as non-saveable. For example: CHGATR OBJ(‘/MYINFO’) ATR(*ALWSAV) VALUE(*NO)
Use the Load Image Catalog (LODIMGCLG) command to make the image catalog ready. Image catalogs with a ready status will be omitted from the save.
In an attended save, you can specify to omit the image catalog directories on the Save Object (SAV) command.
If you have independent ASPs, make them available before ending iSeries™ Navigator if you want them to be included in an Option 21 or 23 save.

Found what you need in the V5R3 manual discussion at:  http://publib.boulder.ibm.com/infocenter/iseries/v5r3/index.jsp?topic=%2Frzaiu%2Frzaiurzaiu2tv.htm
Three times I tried pasting the text and the URL but no luck.  We’ll see if this comes through.
 

I did not mean to suggest that  one would replace the QMNSAVE IBM program, just use the retrieved source as a starting point to write a customised version of the Save procedure.