We changed the signature used to sign our nightly builds to match the signature used on the Google Play version so you may need to uninstall and reinstall in order to get updated.
In most cases it should be possible to backup the configuration, it should be located in /storage/emulated/0/Android/data/com.retroarch/files/retroarch.cfg, reinstall, run RetroArch once and copy it over to the same location.

It’s an inconvenience but it had to be done at some point.