Is this for for sure that nothing can be done about it? I've tried the process because I got the following answer from "timwtheov" on Interact:
"I saw in your other post you had moved in your big flac files in Explorer and then reimported them into MC after having deleted them prior to the move.
However, why not just break the big flac files down into individual flac tracks using MC's tool "Covert Format?" Wer's suggestion of moving to individual flac files is a very good one, as you'll have all the benefits of tagging (saving tags into the individual flac files, for example), plus since flac is natively gapless, you're not going to lose the gapless quality of the big flac file + cue sheet. Convert Format works pretty quickly too, even if you have a lot of albums stored as cue/big flac: I could get through about 2,000 tracks in about 30-45 minutes with my five-year old PC.
It's real easy to do. Try it on an album or two first and then once you get used to it, try a batch. You will have to put a couple of the cue sheets back into MC (and later all of them if you decide to split them all into tracks), then highlight the tracks, right click, select "Library Tools" and then "Convert Format:"
https://pix01.jriver.com/gallery/134ECAA6-6ED4-4647-81D9-0F261024D80F/CF/That will bring you to the Convert Format dialogue where you can choose the options you want. You want flac-to-flac, so "Convert [your number of highlighted] files to: FLAC Encoder," and then you can choose the folder options under "Options." I always choose the same directory as the original file, and I also replace the original file "on disk and in library," as I don't want 2 copies of the same album, but obviously all of that is up to you:
https://pix01.jriver.com/gallery/134ECAA6-6ED4-4647-81D9-0F261024D80F/Convert_Format/Again, try it out with an album or two to start, maybe without replacing the original file in your initial attempt(s), till you're familiar with it."
So if there is no way for JRiver to automate the process of deleting the source file after the conversion, there is no need to reply to this message.