oh well, I guess that you are using the mod of patchouli in boss room + patchouli in library, use just one of then or it can cause some bugs

Also the game doesn't generate an error message or log it in the debug console when this triggers, so I guess it's more likely to be a logic error.

I encountered the same issue with the invisible Patchouli boss. It seems that when you trigger her as an optional library boss by taking a book, she becomes completely immune to all types of damage. So far, I've tested normal tear attacks, Mom's Knife, Brimstone, electric, poison, bleeding, explosions, cards, touch damage, and instant-kill items—all of them are ineffective.

However, if you exit the game and reopen it, the invisible bug disappears. If you exit and reopen again, the bug reappears. On the third restart, a second Patchouli boss spawns.

I don't know what it can be, usually she just take lower damage while a spell card is active.
she's literally immune to damage or you can't hit her?

Sometimes Patchouli can't be hurt and I don't know why，Custom Stage API is properly installed

I'm surprised she doesn't spawn a library pool item for the boss item