Is there any core available that allows you switch disk sides in FDS games?
Nestopia does this. You can switch sides with the L button (I think).
I just wanted to post and confirm what Oggom said. You can indeed switch the disk side in Nestopia (on my xbox 360 controller, it’s L2/left trigger). I’m not sure if any other cores support this functionality for the Disk System or not.
Also fceumm has the functionality, recently added. You need the disksys.rom in your system directory and need to press R to eject the disc, press L to swap sides and press R again to insert the disk again.