I went from H2 to YAML and it said it generated several errors, most relating to "all does not exist" when trying to make a group have the inheritance of all the groups.

v4.1.25

Can you try updating to the latest dev build. I'm fairly sure this issue was fixed in 4773934

https://ci.lucko.me/job/LuckPerms/

Which version of LuckPerms are you using? (/lp will tell you :p)

Can you do an inheritance all command?

Hmmm... It still doesn't work. Let me give you the exact error.
https://pastebin.com/LrLACLBb

You can probably ignore all of those errors. The bulk of your data was applied correctly - looks like those entries were invalid.