If this is just a few albums then you can load both albums into Jaikoz and use Copy and Paste within the main spreadsheet view. If this is for many albums and the filenames of both sets of albums are the same (except for .mp3/flac suffix) then you could do the following.
- Load Mp3 Albums
- Advanced:Export (as .xls)
- Then edit first column of spreadsheet with your favourite spreadsheet tool replacing .mp3 in filename with .flac - Restart Jaikoz
- Load Flac files
- Advanced:Import selecting your spreadsheet
This should import all your mp3 metadata into the equivalent flac files