This issue eluded me for several months until I found this thread on a whim. Naturally, I had spent those months blaming FCP and/or my hard drive for seemingly corrupting everything I tried to import. Ouch!
Is there any other way Sync could be made to handle indexing of these .fcpbundle files a bit more gentle, so as to prevent this symptom, and the need to pause or quit Sync in the first place?