Only trivial issue I have found (android) is with the C1/C2 button settings. When switching back from Litchi to DJIGo they will get reset to unassigned. This is probably related to how Litchi can have multiple setting for each C button depending on which Litchi Flight mode you are in. All the other setting seem to stick between the apps as far as I can recall..
Just dont let your android set either app as the default when you plug in the USB lead. Otherwise you wont be able to launch the other app.
Always use the "just this once" option having chosen either Litchi or GO, when the pick box pops after pluging in the USB.