Old thread, but I have a similar issue.
I have Win10 64-bit Anniv Update (non Insider build). A fresh install of BeerSmith2 (2.3.12). The first step I did was to install the add-on for Blichmann Boilermaker TM (6 equip). I noticed not all of the sizes showed up in my equipment profile list - only the 15, 20, and 55g pots appear. The only change to files on my system at that time was the addition of Documents/BeerSmith2/Updates/BoilerMaker.bsmx. If I then remove the add-on, not only are those three kettles removed, but others from the default/initial load! If I close BeerSmith2, then just double-click the BoilerMaker.bsmx file, BeerSmith2 shows me all of the sizes are indeed present in that file.
I have uninstalled, removed Documents/BeerSmith2 as well as ProgramFiles(x86)/BeerSmith2 and reinstalled. I consistently get this behavior where not all of the add-on "installs" and when removing the add-on, it, plus other stuff is removed. I tried changing permissions, but it had no effect. I noticed that after closing BeerSmith2 a bunch of bsmx files are written to Documents/BeerSmith2. I checked the contents of the Equipment.bsmx file in a text editor and it matches what is shown in the tool. So the application is not properly handling the files.
I can only assume add-ons in general will not work so I am stuck for now.