On AtariAge someone else asked the same question:
http://atariage.com/forums/topic/263360 ... at32-load/I wrote a small binary (very small lol) and put it in a booting ATR. When you put that on a SIObased device (a real diskdrive or a Sio2PC/Sio2SD/Sio2USB whatever) ... and your atari boots SIO after pressing RESET it will reset your MyIDE 2.
A better solution is getting yourself the MyBIOS-in-ROM update inside your Atari. Then you always can come back to any menu (FAT32, MyBIOS, MyIDE 2 cart menu) without a power cycle.
The MyIDE 2 cartridge lacks a reset button. On stock atari's this is the only thing missing on this fabulous device.
With RESET-Proof game on an Atari with stock Rev. 2 XL/XE OS ... a powercycle seems to be needed.
When the game/demo you play from FAT32 is not reset proof, you can use this ATR. After booting this ATR you'll return to the MyIDE 2 cart menu.
The last thing you could try is using the MyBIOS-in-Flash solution. After starting myBIOS get back to the cart menu and run the FAT32 loader. When the game you play does not eat the MyBIOS-in-RAM you might get back to the MyBIOS cart menu.
I'm using an obsolete version of MyBIOS, so I'm not sure if my keycombinations still work on that version.
In my version of MyBIOS it would be SHIFT + CONTROL + TAB -> reset menu -> chose (P) powerup.
Then hit SHIFT to restart cart.