"Nature" Worked, and tree base was indeed the duplicated trees.
- "Nature" keeps track of
- Logs (Non descript, which is why, likely, they change back and forth between uncommon and common on reload)
- Chopped wood (equally non descript, meaning randomly rare firewood you had lodged in your smelter may become common)
- Tree base (0-100% tracking, doesn't remove it properly at 0%, thus it respawns at 100%, right beside the one that spawns by the game, untouched, leaving you with 1 100% and a blank-unstarted tree, which will then become 2 100%s and a blank, 3 and blank, etc)
- All Nature things reset just like Coal to 100% it seems, so maybe the "100%" bug ties in somewhere for each and the fix for one maybe helps the fix for the other?
Edit - Also. Thanks for the info, now I can properly clean up whenever I need to.