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From the RetroArch Wiki…

Disk Changing..
Option 1: To changes disks in-game, go to Disk Options > Disk Image Append.

Some games like Metal Gear Solid require the disk tray to be opened before changing disks. To do this, change ‘Disk Index’ to ‘No Disk’ first.

Option 2 (if the first option failed): Use i-File or i-FunBox or any applications possible to access root file. Go to var/mobile/Applications/ [RetroArch-icon folder] / Documents. Rename [disc1].srm to [disc2].srm in which [disc1] and [disc2] are the names of your discs.

Any more info on how to do it in Retropie would be good..thanks..