A patch is needed to automatically switch the disk's side.
Managed to convert a FDS file to QD and injected it in. Can't swap sides of the disk though.
Zelda II -Link no Bouken handles this by doing a few things.
Firstly, it modifies a subroutine during the disk swapping screen that is supposed to actually check if the disk is swapped. At address $8452 in memory...
This loads the disk drive's status register into A, shifts it right so that the insertion flag becomes the carry, and then if this insertion flag was enabled, it will branch. Otherwise, it just returns and loops, waiting for a disk.LDA $4032
LSR
BCS $8442
RTS
We know already that a disk can't be inserted in VC, so the patch that is used is actually quite simple. It changes the BCS opcode to BCC, which makes the code:
Now even if the disk drive's status register says that there is no disk inserted, we will still branch and continue anyways.LDA $4032
LSR
BCC $8442
RTS
The only other things it does is blank out the "CHANGE SIDE _" and "W A I T" screens to make things a little cleaner.
I don't know how similarly this would work for other FDS games, but I don't think it should be too horribly different. Good luck.