Well I found a sollution from 2016 that worked for me, in this example it´s the snes that made trouble but it works for other emulators too
BuZz ADMINISTRATORS 24 Aug 2016, 17:19
@Robust
Please try the following.
From a terminal please do rm /opt/retropie/configs/snes/retroarch.cfg or delete the file over windows networking
Go to Emulation Station -> RetroPie and do Update RetroPie-Setup script
Go to Manage Packages -> Main section > lr-snes9x-next - and choose "Update from binary"
and all should be good.