Hi Yoav and welcome back :)
I'm not sure it's the same issue but I had a similar issue when switching Artifactory (3.0.6) from built-in database to MySQL. I've exported everything to disk, renamed a ".artifactory/data" folder and imported back after plugging MySQL. Most of jars were imported but some (those that I had to deploy manually in the past) weren't and I had to redeploy them manually again. Also, I think all (or not all, I'm not so sure) our snapshots were not imported as well. So it seems to import actually worked only for a usual third-parties (or may be it didn't work at all and all third-parties were just re-downloaded again?)