it’s hard to say specifically. When you move your project media, is there other media on the target drive? Are you keeping media relavant to a project in discreet folders? Your problem sound initially like FCP is finding media with the same name and connecting to that…. as in, you have several projects worth of media on a drive, with similar clip names for some of your media, and the automatic find is grabbing the wrong pieces. Assuming that all your media is in a single capture scratch folder, once you reconnect one clip, “automatically reconnect all clips in folder” should work fine.