Handling inter-project logic

I manage a large project with multiple contractors. I have combined all contractor programs into one and link off these tasks to get the master program summaries, interface programs etc. When a Contractor updates their program I export all my inter-project logic, delete the old contractor tasks, import new contractor tasks, import inter-project logic.

This has worked well (contractors must maintain Activity ID's) but the master program is now getting too large with these contractor programs that I only need for the references.

I looked into having a stand alone master program with external project logic links to each separate contractor program however I've found some issues in dealing with updates, i.e. when a contractor updates their program and sends me the new xer, how do I re-link it to my master program?