I'm not sure I totally understand the problem here, but a couple of "Beardsworth rules" for Lightroom:
- Never try to resolve problems by re-importing or by synchronising folders
- Once files are registered in Lightroom, only rename them using Lightroom
It sounds like we should take this step by step. What stage are you at, and have you already tried renaming files somewhere? If you do a Library > Find Missing Photos, how many photos does it tell you are missing? Are there any question marks on any folders?