I've download krita-nightly-x64-v4.0.0.51-325-g2126cec79f.zip, and when I run it most of the brushes that I made had desappeared ; When I opened Krita 4.o.o beta 1, those brushes also had desappeared from their normal location, Duarte's Bundle... Thank's god they still were located in "All" tag and I was able to get them to the normal location.
If I had installed the EXE. version instead of the Zip, I think they would be lost for ever. Better look for this issue before lauching the final 4 version.

No, I don't think your brushes disappeared. What did happen is that this build has a updated version of the tagging file format, so the tags weren't read. That's something we'll have to warn people about, but you didn't lose your brushes.