If that doesn’t help, I would go to $OMD_ROOT/var/check_mk/background_jobs on the checkmk server and see if I find someting with your ID d0af90fb-5ad2-43e0-b084-6fd1573ceaff and probably just delete it. It might be neccessary to stop the site before doing so and start it afterwards.
OK, That was nearly the solution.
I had a look at the background jobs, and found this:
PermissionError: [Errno 13] Permission denied: ‘/omd/sites//local/bin/nvdct/conf/nvdct.toml.orig’
That file was owned by root, not site user. I did chown, and now activation of changes works.
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This helped me with the exact same issue; a file in a plugin package I’d build out had the wrong permissions set, (600, root:root). Changed that to 600, checkmk:checkmk on the live system and config updates work now. Going to update the package now.