After some tests, I wanted to start over. So I removed the directory atlassian-stash-1.0.0.beta5 and the stash home directory.
Then I unpacked the atlassian-stash-1.0.0.beta5.tgz file again and put the stash-home dir in the setenv.sh again.
After starting stash, I was really surprised that all my old settings were still there. Probably the HSQL database is stored somewhere outside of these locations.
The problem is that I cannot remove the old projects since Stash can't find the files in the home directory.