Thunderbird deletes all emails at random times but is set to "never delete" them.

It always deletes them when the program is closed and sometimes when it is minimumized. Also deleted them from the archives folder. Most seem to be in the "Trash" but not all. This started at the last upgrade.

Ok is the account IMAP. That is the key.
If you go to the troubleshooting information on the help menu and look at the mail and news accounts there will be either an IMAP, POP3 or SMTP entry for each account in the name.
If it is imap, then the protocol is synchronized ie the imap phone, Thinderbird and what you do in your browser all replicate to one another.

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