I have a laptop running Ubuntu 20.04 with Thunderbird 68.10.0. It connects to my gmail.com account and also a linux IMAP mailserver with my university. For the university IMAP account there are two sent folders, one called "Sent" and the other called "Sent Messages" No matter what I do I cannot seem to reduce this to a single "Sent" folder.
I have tried:
right click on "Sent Messages" to delete it. Sometimes delete is not an option when I right click. Sometimes it is an option and I delete the folder, but it is always back when I restart Thunderbird
deleting the copy of the folder in my .thunderbird/[profile]/ImapMail and deleting the copy on the linux IMAP mailserver. When I restart Thunderbird, it is recreated
unsubscribing the folder. When I restart Thunderbird, it is back and I am subscribed again
in Edit->Account Settings->Copies and Folders for the gmail account I do not have "place copy in" checked. For the University IMAP account I have "place copy in" set to '"Sent" Folder on IMAP account'
removing "Sent Messages" from the "subscriptions" file in the Maildir folder on the university linux IMAP mailserver
all of the above with "Sent" and "Sent Messages" reversed.
My older computer running Ubuntu 19.10 and Thunderbird 60.9.0 connects to the same accounts and has the same problem. My wife's Ubuntu computer with Thunderbird and only one email account set up has the same issue.
Your university IMAP may by default seems to use the name "Sent Messages" to store send mail. The IMAP server may be set not to allow to delete it.
In Thunderbird, you can define what folder to use for sent mail ("Preferences - Account settings", in the "Account settings" dialog, locate your account in the left pane and select "Copies and Folders"). You recognize the folder used by Thunderbird by the special icon of that folder.