RetroDECK is completely standalone/sandboxed nothing will clash, so I believe they can coexist.

Not automated, but neither that hard to do: I believe the roms folders got the same names more or less. About the save/states we split it by system and emulator: to retrieve the structure you could just run a game once, save and understand the path, it’s pretty straightforward. However if somone wishes to contribute a migration script it would be great.

You can update it from discover, by going into desktop mode.
But if you are coming from a really really old version it might be better to just reinstall.