I recently had this same problem on a project where I had “borrowed” alot of media from other projects on the system
without going through media manager to create new copies. In many cases, I was even utilizing media that was captured
for “project A” then borrowed for “project B” and then borrowed again for “project C”. I was never able to recover the lost
timeline, but the pro support people from Apple agreed that this might be a problem depending on how many layers
were involved, and if any of the media was nested. Long story short, they recommended going through media manager
to create clean copies of the media – especially if alot of media was being accessed from different source files.