I think your SOL...unless the new file has exactly the same filename (at a minimum). Just overwrite the old file with the new. MC will never know the difference (to be safe, make sure it's not running). Some things such as bit rate, file size, duration, calculated fields, and RG values will be off (inc tags if they didn't match), but updating the library and re-analyzing should correct that...without losing your play count. I believe that MC indexes records based on filename.extension only, so it should work.
10-27
edit: Using MC to rip will probably throw your play count out of whack (it will reset it to 0, since the new rip matches an existing record). Therefore, use another ripper (such as EAC) for this task...then do your overwrite. If you're new to EAC, then I could send you the rip profiles I have built (with the correct tagging parameters) for ogg, flac, ape, & mp3.