I know this is an old thread but i am just now running into this exact problem.
I wanted to change all SNES games from SNES9x to Retroarch in order to get Retroachievements running. Changed the emulator with ctrl+a and the wizard for all SNES games which worked fine. Retroachievements only supports select versions of ROMs though and sometimes my default version would not be supported, but maybe another one. But if I tried to run an alternative Version of the ROM it would always start it with SNES9x and not Retroarch. (I even removed SNES9x in an attempt to make it run with Retroarch, which failed.) I know i can change the emulator for specific versions of single games in the edit menu but i was looking for a way to do this for all my games at once.
Then i looked the problem up and found this thread.
This was an option i was considering but i thought that merging the games again might be a hassle. I don't know if i'll have to do it for each game manually and how long it would take me to do it for a big collection.
So my question is: By now, is there an easy way to change the emulator for all Versions of all ROMs on a system in one go? Or should i go with the expand -> change emulator -> merge path and how long do you think it woult take me to do that for a big SNES collection?
A quick answer would be greatly appreciated.