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Dig uses its own copy of the RetroArch config file, so if you change settings outside of Dig, Dig won't know about them (and vice versa). You can update Dig's copy by selecting "Reset RetroArch config" in App options.
If we can't use retroarch's config file then we need to know what the default buttons/keys are to bring up the Retroarch menu mid-game :/
When Dig first runs it creates a copy of the config file for its own use, so all your RetroArch settings are preserved at that time. When RetroArch is launched from Dig and if you change settings, the changes are saved in the copy. If you run RetroArch outside of Dig, changes in settings are save in the original file. If you want to use those settings in Dig then "Reset RetroArch config" will copy the current config for Dig's use. I hope that's a little clearer :)