Maybe I can help.....I had the same problem, and I truly loved my custom brushes I updated, and the first thing I went to use was my custom brushes mini, and couldn't find it. I tried everything, including re-downloading, to get it to work, and NOTHING!!!!. I had it all installed in the correct folder, and couldn't figure out what I was doing wrong, so I came here to search for an answer. I saw a reference to an install folder, but couldn't find it. For some reason, I ended up with a second Paint.Net folder, with Paint.Net 3.36 .exe and a couple of other files in it. The exe file for the custom brushes was in there....dragged and dropped, hit the .exe once it was in the "good" Paint.Net folder, and now I have my custom brushes back! I hope this helps others who may have the same problem...
By the way, this truly is a great plug-in