This seems to be close to the prototypical application for Master/Subprojects. Yes, they are very susceptible to file and link corruption, but they seem to work for some people.
Based on some other forums, there is a common recommendation to create a new, empty master/consolidation project, then add all the other projects to it as linked sub-projects. Then analyze away. The file corruptions come into play after you attempt to save these files, give them different names, move them to new directories, etc. So one recommendation is to never save this bit.
So far I have had reasonable success keeping a master and four or five sub-projects in a common folder, then archiving the entire folder (to .rar or .zip file with its own date/name) on a monthly basis. Sharing out sub-projects for updating by others is always the plan, but the details never seem to work out that way. Merging different subproject versions back into the master is definitely a headache….