Just start the retropie_setup script again and select source install.
In the list that follows you can mark every emulator that you want to be installed (by pressing space), but that will take its time again so…
If you want it faster just select the binary based install and remove all the emulators you don’t need. If theres an update to one of the emulators you can still select sourcebased install and only install that one.
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