I’ve added a custom component (integration) and there seems to be a fault in the integration. Now I have more then 5000+ entries.
Is there a way to delete? Obviously, manually is not an option…
The spook integration have some options for programmatically removing devices and entities.
Read the documentation linked on the GitHub page!
NO ONE has a legal license to use Spook.
Read the license…
True, the license has become rather relaxed lately.
You will not start WW3 anymore by using it. 
Unfortunately, SPOOK only has the ability to disable integrations (I’ve tried via Developer Tools > Service) and has to be done manually.
With 5000+ entries/integrations this is not an option.
Also I wish to delete instead of disable… Any thoughts?
It should have an option to remove orphaned entities.
Yes,
Tried to run it 2 times now (after making a backup 
), but nothing happens?
Don’t even see a (DEBUG) log entry which indicates the service (Home Assistant Core Integration: Delete all orphaned entities 
) is started or running?
I have never used it, so no idea how it works, but I think the developer tools → service shows the possible settings for the call.
If it does not remove anything then it might bebecause the entities is still linked to an integration and you need to remove those instances then.