It's easily done if you rename the folder...
ssh in and
every setting and add-on is now stored in "kodi-bak". But Kodi won't recognize this folder anymore.
reboot after the command above and Kodi will create automatically a new .kodi folder with all settings at default and no add-ons/repositories installed.
Then test if the issue comes up.
if it doesn't come up, install one add-on after the other, to see when (or if) the issue comes up then.
if you want your add-ons and settings back for a moment...
ssh in again and:
Note: the text after the "#" is just a note for you and not a command to enter.
reboot after you did both commands and you should have your add-ons, repos and settings back.
Greetings