Issues with permissions

Hello… I have run into a massive problem with permissions that I cannot seem to figure out how to solve. I recently set a bunch of permissions from different assorted plugins to true using LuckPerms, and then restarted my server due to connectivity issues with some of my members. Keep in mind this is on launch day, lol. So we restarted, and all of the permissions that had previously been working before the server restart no longer worked. Everything was broken. However, LuckPerms still registered it as true for the default group having those permissions that I had set before the restart. What is the issue here? I really cannot figure it out and this is a huge headache. Any help of any kind would be greatly appreciated.