I wanted to rearrange my skills without cheating to much, so I reset everything to 10 and was planning on increasing them from there. But if I put just 1 experience into any skill now it will instantly go 100. It seems the advskill command makes it permanent? any fix for this?

the console is a dangerous tool to play with, I have used it to advance skills for testing purposes but never to reset them and then try to advance them again. Remember the game was not intended to work in a backwards direction and that could be the cause of the problem.

One though though did you remove the perks when you reset the skills?

Yes, load the save from before you messed around with your character.

This also works!

I saved right after I thought everything was reset, and I don't use auto save files. Lost 100+ hours, time to start a new char now

... and put back the auto saves...

So, what you're saying is, you played for more than 100 hours without saving then you messed with the console and then saved right away??

Or do you only use one save game slot??

If you are worried about save files taking up space then I'd suggest using a minimum of two save slots. Alternate between the two. Then you have your back covered. Otherwise you should be aware that using only one slot can have massively negative consequences, especially if you are diddling with the console stuff.

bad idea to mess with the game, you should have started a new one