Sorry about my english...
For server-admins, having issues with blank recipes (not only an Pythagoras Problem), there is an other option to fix this Problem.

1. Stop Server
2. Download game.db
3. SAVE A COPY IN CASE OF SMT IS GOING WRONG!
4. Open game.db (I am using DB Browser for SQLite)
5. The Table item_inventory is storing the inventory of everything including player-feats-list. If u are admin. Enter admin mode and have a look at the id´s of the blank feats. You need to write an SQL-Statement to delete these ID´s (Table: item_inventory Field: template_ID) where the owner id is a player.
6. Simple way: Delete all id´s that are causing problems without any check of the owner. If the owner is not a player an item with that id is stored in a loot-box or someting like that. Deleting that id will delete that item but thats not that big problem as a corrupt feats list.
7. Save game.db
8. Upload to server.
9. restart server.

Thats how i fixed that... ;-D

What are some of the IDs of the recipes that weren’t removed?

Recipes are stored in your game.db; removing a mod will not remove that recipe entry from the character. Unfortunately, CE uses an awkward means of resetting your recipes. Yellow lotus appears to only clean the recipes that are attached to a feat. This means that the mod must be active and the character must have the feat for the associated recipes to be cleared. As far I know this will be a problem with any mod that adds new recipes.

It is best to always use a lotus potion before removing a mod.

Yeah seems this screwed up my game :S
I tried making Pythagoras inactive and then use the clean up along with the lotus but noticed some empty spaces in my recipe list still stating there are recipies and sure enough when I actived Pythagoras again, all those empty spaces were filled with the recipes that my character had before but shouldn't have since I used the lotus.
This isn't the first time that Pythagoras causes issues and seems your mod really doesn't like to be removed or triffled with in single player since it will linger and cause problems after removal. :p

@joshmiller83, No the changes should only affect old characters that had bought the old recipes.

We are planning to wipe characters but not the server/structures. Is this mod needed at that point?

Thanks for letting me know.

hmmm for some strange reason, using this screwed up my weapon racks and shield displays.
I can't make the shield displays or the vertical racks, they just eat up the materials even do they can be picked from the admin panel. But with the normal weapon rack and the others, none of the weapons or shields are being shown.

worked great.

Well, that explains the blank recipes. well get it and run it.

Good work!