Email accounts on your own server

Not sure if you have got this sorted but had the had issue with email accounts that were created on our own web server.

I used to be able to disable the account, log into webmail & delete any additional folders that had appeared then re-enable the account & there was only the inbox under all inboxes.

The only way I can do it now is to delete the account from the server (after having saved anything I wanted to keep first) then re-create it & re-add it to my desktop.