Hi @mbuchberger1967,
There has been a major change since I wrote the original post with regards to how OH2 stores the configs. See here:
Many of the commands in the original post still work but they are more related to bindings and their configurations (not so much for items, sitemaps, things, etc)
I would go the way that @Udo_Hartmann recommends (keep your customized configuration files and reinstall)
Another way would be: Karaf console, then:
smarthome:links clear
smarthome:items clear
smarthome:things clear
This will clear out whatever OH2 has stored internally. Make sure that you have removed the _default files, keep your files in the configuration directories and OH2 will re-read them and populate the internal (json) database.