is your account IMAP? If the answer to that question is yes. What is your mail providers retention policy for inbox messages?

No don't think the account is an IMAP. The email account has been set up on each device and I cannot access emails from the internet without setting up the account. I also have a laptop and none of the emails are deleted from that, and they go back to 2019. The problem started when the desktop hard drive failed and windows 10 needed to be reinstalled. I hoped there was a setting somewhere in thunderbird that was causing the issue. Thanks

Sorry to confuse. Yes it is an IMAP Server. However as I have said above there is no problem with the laptop. On the account settings both computers are set under storage to "don't delete any messages". There is also plenty of spare capacity on the hard drive.

Check the laptop account, it is probably set up as POP which is not subject to synchronization to the server after download.

You are right the laptop is still POP. Can I change the desktop back to POP or is there a better way to automatically archive all of the emails before they ore deleted? Thank you

well the first thing to check is what your choices are with your email provider. If it is only the inbox, it might be you have to make a choice in that 3 weeks to either archive (which will move the mail from the folder), delete the mail or perhaps move it to local folders so it is removed from the mail server completely and no longer under the control of your mail provider.

Or you could just add the account again in Thunderbird as POP and it will behave as your laptop does. Once you have the POP account working as you like it you can remove the IMAP one from Thunderbird. Just note that doing so also removes all of it's folders from view, so if you have mail in say the accounts sent folder you might want to copy it somewhere local before you delete the IMAP account from Thunderbird.