Given that any enhancement to FM on this won't be released by sundown, when I used to encounter it, there were two approaches I found useful:
On the presumption that the document at one time worked correctly, try to figure out where it was at the time (in relation to the now-broken filepaths). Place an original copy of the .fm file(s) there. If it opens, re-save to the new location, and presto, all file paths are updated.
Create a new ./imports/ dir under the current .fm file location. Copy or symlink all the know imports to there, and FM's "use new path" dialog should find them all on the first dialog pop.