I was having the exact same problem but with the PC Engine -> TurboGraphix 16. Thanks to this thread I've finally got that resolved!

Hello and thanks for the answer again. Every emulator, even if I enter Retroarch to move between commands I have to use the controller 2 instead of 1. Image the last one, 4.4 and about the retropie version don't know what you mean, I have updated the script but don't know about the version, how do I see it? Sorry and thanks again.

For information, I formatted my root partition with F2FS more than a year ago, and never had a corruption since.
The main drawback is that it's more difficult to resize ATM than ext4 or xfs.

@dbg33k This would work except i think you would run into issues with resolutions and screen sizes. Your hand held will have a small screen and probably need to be set to a lower screen resolution. It might be a pain to constantly change the setting back and forth between your TV and your handheld as all of those settings are also within the SD card. I might suggest that you buy a micro or mini usb drive and transfer your roms onto the USB. Then you can have small SD cards in both your pi's and just move the thumb drive back and forth. With the small thumb drives it shouldn't be to much of a problem with the handheld. All the roms and save files will be stored on the usb stick. Here is an example of a 32gb stick link text