I'm not sure what you mean by the "cue files" part of your question, however... If you have a set of files that are MP3s, and you re-rip them to individual FLAC files, you can easily update MC's library to point at the FLAC files instead of the MP3s.
You can "replace" the files in MC by using the Library Tools --> Find and Replace tool. First, make sure to copy the new FLAC files into the proper location, and move (or delete) the old MP3 files somewhere else to get them "out of the way". Then, open MC and select the files (which will all be broken now) and do the Find and Replace, have it change the Filename tag, and replace all occurances of "MP3" with "FLAC". Next, you simply need to change the File Type tag for those same files from MP3 to FLAC.
That should fix it. As I said... I'm not sure what you meant by the CUE file stuff. Did you re-rip to one big FLAC with a CUE sheet instead of individual FLAC files?