You can swap ATRs (for two-sided disks, etc) using the swap button on the XEL-CF3 as well, as with the SIDE2 swap button.
I was just reading up on doing this! I need a MAP file containing a simple list of disk numbers and files to mount like this
D1:GAME Disk 1 Side 1.atr D2:GAME Disk 1 Side 2.atr D3:GAME Disk 2 Side 1.atr D4:GAME Disk 2 Side 2.atr D5:GAME Save Disk.atr
on a 2 atr title, pressing the button just swaps d1 and d2, what happens on a 3 or more atr title?