Some time ago, it came to my attention that someone has altered a certificate in Plesk, but seems to have chosen the default. Since then, on every site that uses the certificate this apears under "Physical hosting" -> "Setup".

I have replaced the name of the site bij 4 times *.
Anyway, I did not care much but yesterday a client approached me complaining about him being logged off while he was trying to erase a database, with the notification of a certificate problem!
Besides that problem, I would like to get rid of the last part of the certificate name(Repository)... I've tryed deleting the certificate from the domein ****.nl but that failes because sites, and IP's are linked to it. Also from the Server -> Certicates it will not delete...

 

If I understand you correctly, you want to delete a certificate. Actualy certificates in plesk linked to IP addresses, not to domains. So to delete certain certificate you need to remove all links between that certificate and all IP addresses.