There are many nasty bugs in regards to relinking media files in FCPx. Many things that have not been explored properly. (Normal for such a new software).... It would help (me) a great deal if were to describe the EXACT steps you took DURING relinking. And WHY you had to relink....
Without that it is more or less impossible to help you. I would have to guess. What you are experiencing is most likely a BUG (not necessarily though) and if you can provide detailed info about your steps to achieving the problem then you should post it here as well as sending it to FCPx Feedback. They (Apple) REALLY listens to it and they are really forthcoming in trying to solve problems.
General Rules for Relinking
1) DONT EVER relink while you are in Proxy Mode
2) If after relinking you are experiencing "Funny Stuff" >>> Temporarily move the contents of "Transcoded Media" of the event library in question outside of the event library... QUIT FCPx first... Then restart FCPx to check if the problem is gone. After than PUT BACK the contents.
IF you have had FCPx create high quality media for you, then after relinking you MUST CREATE it again(If you were relinking original media). Unless the file you are re-linking to is PR 422.
3) If other problems arise > Select the Event and from the File Menu "Delete Event Render Files" ALL
I had one instance where my employee had stabilized a few clips in After Effects... He knew no better and saved all his After Effects files i.e. MVI_9889.aep (Which is merely the project) into "Transcoded Media/High Quality Media" after doing so... FCPx thought that those .aep were movies (Even though he never added them to the event library) and displayed them with a RED icon stating that FCPx did not have the necessary plug-in to playback the movie....
Just one example of weird stuff going on with the media management....
Rule of thum.... DONT (unless no way out) mess witht ANYTHING inside the Projects or Events from the Finder.... ALWAYS do SUCH from within FCPx.
And if you find any anomalies - report step by step to FCPx Feedback what happens... So that we can get rid of those bugs
PS - another problem is when FCPx has created High Quality Media for you.... When you select YOUR clip in the event browser. You are actually selecting a PR422 files that FCPx created for you. If you re-link THAT file to another file, FCPx wont actully delete the PR422 file. And I have had numerous issues where it (FCPx) would get confused afterwards. And still USE the original PR422 file.. Just because it was there. I had to quit FCPx and physically delete the file via the Finder for FCPx to actully use the clip I had re-linked to....
I take that FCPx uses UUID (Unique User IDs) for each file... Becuase if you quit FCPx and swap one file that it is using with an exact copy of itself, FCPx will still throw a "Missing Media" icon. UUIDs are great in some scenarios and killers in others.