There is some very suspect behavior with service programs and stored procedures at V7R1. I'm not sure this is exactly what you are describing, but here's my issue:
We have service programs (a number of them actually) that each contain 7 or 8 modules. These modules are each related to a table. Each module has exported procedures for get, get list (result set for a client), add, update, delete, and possibly some specialized ones. Also many private procedures. So that means, for one service program, possibly 40 or or more exported procedures that reference SQL procedure definitions. When I promote (through turnover) from dev to test or from test to prod, a large number of SP definitions get deleted. I'm not sure if this is a TO, IBM, or combination of the two that is causing it, but the upshot is that the SP definitions disappear, and the websphere and c-sharp guys start crying, as that is the interface to the system.
I then have to check out all the missing SPs, and run them back up through TO after the SRVPGM to restore everything to it's normal status.
Looking at SYSPROCS, I still see my procs, but with changed library names, usually those TO uses for rollback purposes on a form if it goes into recover mode.
My only solution has been a brute-force method of doing an exception join of QSQLSRC in the to environment to SYSPROCS to see what got wiped out. I then check those out, promote them and get back to a matched relationship between SP source and registered procedures.
I'm sure IBM is trying to do something to help those who restore libraries to a remote system without change control, but the 32-procedure limit and the strange behaviors aren't doing us any favors. It would be nice to be able to control the behavior, possibly with a parm on the SRVPGM create, system value, something? Anyone see anything similar?