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Are you sure they are the exact same plants? The game spawns new ones (up to a maximum) while you're not playing. Depending on what it picks, you could either get new copies of already catalogued species, or entirely new things.

Glad you're enjoying the game.

Positive that they're the same, I did a few remove-reload sessions of a couple in a small area to make sure.

If you want, I can try taking a look at it.  If you are on Windows 10 (I can no longer support Mac) send me your save files (you can find them at C:\Users\"account name"\AppData\LocalLow\OwenBellGames\Mendel). Describe exactly which plants your removing and I'll try and recreate it. It's a long time since I've touched the game code and I'm busy with other projects, so I can't guarantee I'll be able to fix it, but I'll at least see if I can find the bug.

Mendel Save Thanks for your time! The offending plants will be the "New Species" nearby when you load in.
Things I've tried: Moving the plants works, but even moving and deleting them will just have them reappear in their new position. Naming the species doesn't prevent it from reappearing, and I backed up this save and started a new island, the issue persists on the new island. I can confirm that I used to be able to delete plants, so if there's just been a hiccup along the way and a fresh install is the answer, well there are far worse things.
Thank you very much for your time and responses :)