For me, the task here is to find the MP3s that are *duplicates* of the FLACs, and get rid of the MP3 versions from MC's library. One way to do this is to use the built in Smartlist at:
Playlists > SmartLists > Audio - Tasks - Possible Duplicates
Then sort that list by Artist, Album, File Type, and Track #. Click those in reverse order, going right to left and it should sort as I wrote it left to right. That's how MC's sorting works: You have to select the order in reverse.
Once you've done that, you can go through and select and delete all of the MP3 versions that are exact matches. This makes it a manual process, which is better in some ways because *you* get to choose what to do. If you have more than maybe 30 or 40 duplicate albums though, this might become kind of a long task. Someone else might have a more sophisticated way to make this more automated.
Good luck with your task.
Brian.