That is indeed your bios path? And you don't have aes-bios.bin in that folder? Is something moved?

What does:
ls -l /home/user/MyDocs/roms/Bios/
show?

This file was always needed, only the fullscreen issue is changed since the last version.

And remember everything on your device is case sensitive.

Bios path is default placed on /home/user/MyDocs/emu-roms/neogeo/bios, so the update can not have overwritten this setting.

edit: aes-bios.bin should not be needed if universal bios is choosen. What bios do you have selected in gngeo-gui config?