It sounds like you have removed files that you need, like the retroarch.cfg file, can you start a fresh with 3.0?
If you need to keep your current setup, try zipping your configs and upload as an attachment – I could probably then list the issues.

zip -r /opt/retropie/configs/all/config-details.zip /opt/retropie/configs/*

That puts the zip file in the dir above which is browsable from windows.