maybe try to create an appropriately sized ramcart in fusion, load it up, then use the internal Sega CD manager to copy your savefile to the new ramcart and use this with your Mega SD.
the filesize should be 8 KBytes, unless it's a ramcart file, then it could have 16KBytes or more. if your savefile size is different, then maybe it got corrupted somehow?
found an old topic here
. apparently somebody had some luck with a similiar issue by using RetroArch to manage their saves.