Modbuddy project out of sync with folder structure?

[carnivorejoe]

So I must be missing something obvious. I haven't looked at civ 5 modding in some time and I've probably forgotten some basic functions of ModBuddy, but I made some changes to a project in ModBuddy last night, opened the project up today, and none of my changes are reflected in the project structure. I think I forgot to save the project before I closed ModBuddy, so that may be what caused the issue, but all the new folders and files I created are there in the project path like they should be, and the ones I deleted are not in the project path. They're just not showing up in ModBuddy. To make matters more annoying, when I try to recreate them in the project, I get an error saying these folders already exist... what am I missing?