I'm starting to clean and merge my cc and I've been converting sims3pack cc to package files (using delphy's cc converter) since it is easier to install and remove and can be merged. But is there any type of cc that can't be/doesn't work when converted? Patterns did not work when I converted them but are there other things that don't work either? Such as build objects like windows and usable objects? And what about lots with cc on them can those be converted?

Patterns made with the CAP tool may not work when converted to package files, but they can be fixed manually. There is a comprehenive guide here: https://ktarsims.tumblr.com/post/15...oarder-tutorial (have a look at section 5.
Counters (and other modular objects) may have some issues when you try to use CaSt on them, but that doesn't break your game.

Lots with can be converted to packages too. Unpacking them will result in several package files with cryptical names. You will have to find the file that is the actual lot (which belongs into the library folder as nitromon already pointed out) and then can decide if you want to throw those additional CC packages into your mods folder or not.

Personally, I convert everything to packages. It also allows you to control what is in your game and avoid CC you don't want/need/that is corrupt.