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Hmm... What sorts of links are being broken? By that I mean, are they xrefs
from one .fm file to another .fm file? Xrefs within the same .fm file? Table
of Contents entries? Across-book links to specific sections?
No guarantees that knowing this info will help solve the problem, but it
might point to something that isolates the issue.
Also, are the links reported as broken in FM or is the issue just apparent
in a subsequently-created PDF?
And maybe there's something odd with this one book; can you successfully
rename files in a different book?
(When I googled "framemaker renaming file breaks links", the issues that
popped up seemed to be about cross-book links.)
Also, when you regenerated the file, did you do that for a single generated
file, such as a ToC, or was it via the Edit > Update Book option? That
latter is what I've found to be most reliable, across many versions of FM.
(It might help to know which version of FM you're using.)
And I second Lin's suggestion to try the frameusers list.
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