I now tried to reproduce the problem, and I cannot. Normal Ack’s can be deleted. 
I am using “Checkmk Managed Services Edition 2.1.0p18”.
Perhaps the problem was solved. I will watch out for old ‘acknowledge messages’ when they pop up again and will try to delete them as well. They only pop up if something is not OK, which can take a while.
Not sure, if it solves the problem reported by @bitwiz as well, so please do not close the thread.
Update: In the meantime, I found out, that the old ack messages are still there and I cannot delete them. So, probably, I have marked them as persistent. Looking forward to werk 15255!