I don't believe there is way to rename files from properties from cue entries regardless of the format.
You will have to find the filename, presuambly the big FLAC file, then look for Filename (Name) field in the action window or if you have added as a column in your viewschemes, you can edit it directly there.
Now the cue items will still be pointing to the older name. If you look at the status bar, MC will say File not found, ignore it. You will have to do a Find & Replace on the cue item filenames. Select all cue item filenames, for find enter old filename & replace with the new filename.
Again it helps matters a lot if you have field Filename (name) added to the viewscheme used for editing, im my case it is Playing Now.
There is one *gotcha* to this cue thing, pay attention to the cue item file names when you do any renaming operatoins, if all went well it wil say
cue_item;1
cue_item;2
..
cue_item;n
where cue_item is the same as the *new* filename you have given for the big FLAC file.
at no time should it say
cue_item;(1)
cue_item;(2)
..
cue_item;(n)
If this happens then you have a cache filename collision, that means MC has got confused because you are giving an item more than one filename. Immediately do a Undo or Ctrl+z, restart MC and repeat the cue item rename operation. Restarting MC clears the cache and the rename should then take.
Another tip to avoid this (1) stuff from happening is, to avoid doing a Locate inside Media center before renaming.