I don't think the bufotenine is lost. I think it's either bufotenine N-Oxide or more likely bufotenine carbonate that's forming.
Mescaline freebase eventually forms mescaline carbonate if left out in the open. It’s a solid, and very active. It can also form mescaline N-Oxide which is a reddish brown sticky mess, like most N-Oxides are, and that isn’t active according to SWIM’s tests. Bufotenine freebase has a similar pKa as mescaline, and so it probably also forms bufotenine carbonate when left out in the open.
I think more than likely the freebase bufotenine is forming bufotenine carbonate, which I believe is black, and that’s messing it up. The salts of bufotenine that SWIM tried are all unpleasant, not very visual at all, and bufotenine carbonate probably is too.
I don’t think it’s oxidizing. Bufotenine N-Oxide is very nauseating and sticky. You’ll feel like you were hit in the stomach if you smoke it. Yuck.
The seeds don’t contain freebase bufotenine, so they would not form bufotenine carbonate ever. But they do have bufotenine N-Oxide in them, and sometimes a lot. This is the main “toxin” present that makes you feel sick in the stomach. It’s a sticky substance and its presence often prevents bufotenine from crystallizing properly during extraction. Older seeds should have more bufotenine N-oxide as the seed ages. Bufotenine N-Oxide should take longer to form than bufotenine carbonate, unless it's very hot where you live.
Old black nearly inactive bufotenine can be renewed usually by dissolving it in acid and then freebasing it again. When dissolved in acid, it bubbles, just like when you add acid to sodium carbonate. This indicates to me that the old black bufotenine is bufotenine carbonate and not bufotenine N-Oxide. You can’t renew bufotenine N-Oxide by simply dissolving it in acid and freebasing again, you need to reduce it using zinc or something similar. But you can renew the old black bufotenine by dissolving in acid and freebasing it again.