In order to answer your question precisely you would have to provide a lot of additional information.
1) what is your camera original?
2) is there camera roll metadata for each clip and is it different for each card you imported?
3) have you checked your sub-clips to make certain they have timecode, and does proxy timecode match timecode on the camera original?
4) is there a pattern you see that you did f’ed failed to mention to us with regard to which clips relinked vs those that did not?
(***I’m not certain if Premiere handles subclips better than FCP 7 did, but I can tell you that most experienced online/finishing editors who ever experienced working with subclips in FCP would advise anyone to avoid using subclips in any online/offline workflows.)
David Roth Weiss
Director/Editor/Colorist & Workflow Consultant
David Weiss Productions
Los Angeles
David is a Creative COW contributing editor and a forum host of the Apple Final Cut Pro forum.