I suspect they should work together though I have not tested it.
What I suspect you could be running into is one of two things:
1. IAP-9x is limited to 16 IAP per group. All other models are unlimited.
2. IAPs must be in the same Vlan........are the two parts of your building in separate Vlans? If yes, they will never see each other.
Just thinking out loud now, since all APs must run the same version of OS there could be an issue there. Try the first two items first and let us know how it goes or provide more details (vlans, versions of code, etc.).