I have a fairly extensive overhaul nearly completed for a couple of the perk/skill trees. The only issue I'm having now is with my existing, level 50 character whom has maxed level perks in the areas I'm working. I can't tell exactly what's going on, but my best guess is he's still keeping the bonuses of those old (vanilla) perks, despite them being gone from the skill trees. I tried removing my mod and installing another (by someone else) that's similar, but had the same problem with it too.

Are there solutions to this sort of problem?

Hm, last try, then I'll assume it's not fixable.

If your perks are completely new, as in you didn't just modify the vanilla ones, removing the perks from the level up screen won't remove them from the player.

You'll need to remove the vanilla ones manually via the console in game or papyrus in your mod.

This might be a saved-game problem.

Are the perks - and so the abilities they give - stored in a saved game file?

(I haven't tried, so I don't know ... but it does sound like they might be)

If they are saved, then - as said above - you would need to check the PC in your script and remove any offending items

Oi, I don't think I'm ready to mess with scripting yet.

Hey, if I were to modify all existing perks and mold them to suit my needs, would that fix this problem?

It depends whether the "attributes" a player gains from a perk are stored in a saved game.

If they are, then the only way to make your MOD "Save Game Compatible" is to remove the perks you don't want from the PC. Which means learning scripting.

I would urge you not to amend the Vanilla Perks, unless there is no other choice as it will almost certainly lead to problems for you and your players.

Is there an easy way to tell whether a perk is attached to your saved file, as opposed to getting its information based on what's in front of it (i.e. modified perks)?

Just trying to save myself some time before I spend hours fiddling around with something that may not even work.

edit: yeah, changing the vanilla perks, or rather in my case erasing their data, seems to do the trick.

As far as I know, there is no list of what is saved in a saved game file.

From other similar topics, my guess would be that PC perks are saved, though