I solved this by downloading a new rom of Fire Emblem Sacred Stones (USA, Australia version) and patching the .ups file of the newest version of Vision Quest to that. Then I set the save mode to "sram" and selected "boot with addon". This works with both regular saves as well as suspension saves for me.
I don't know if the issue was caused by patching to a broken/bad rom or if it was incompatibility between the patch and the European version of the game that I had used before, or if the patch I made first was corrupted somehow, as using sram save mode and boot with add on alone did not work for me. I recommend first trying to change your save and boot options, and then installing a newly patched version of the game.
OP probably doesn't have this issue anymore, but I couldn't find another solution online, so I hope this helps someone who is also struggling!