Hey Ryan!
Thank you for checking out my game and for the lovely feedback!
In an older version of the game, plants would despawn if you pressed E while sleeping. That was actually a debug function I forgot to remove. But I’ve fixed that in the latest versions. Did you download the game recently (in the last 7 days), or could you be playing an older version?
Plants also despawn if you don’t water them for two days. Unfortunately, I didn’t have enough time to make that clear to the player. I had planned to add a dry-soil model with a withered version of the plant instead of just making it disappear.
Fully grown plants can only be used a limited number of times: Sickle Leaf 3 uses, Fire Lily 2, Bombkin 1. After that they disappear from your inventory (which also isn’t very well communicated to the player. Syll does mention it when you "attack" her with the Sickle Leaf, but not everyone ends up doing that, of course).
If you don’t mind, you can send me your save file on discord (I left you a message there).
You’ll find it here:
C:\Users\USERNAME\AppData\Roaming\Godot\app_userdata\FarmJam\savegame.json
Then I can check if anything weird is going on and restore the missing plants!
Thanks again, and kind regards,
Oakhardt