There is a file, one per account, named msgFilterRules.dat which can be opened in a text editor. You'll need to read it through carefully to work out the pattern and then choose and delete the set of lines corresponding to your unruly filter.

The symptoms suggest that Thunderbird is successfully removing the filter from memory, but is unable to modify this file, so the filter disappears immediately then reappears on the next restart.

The msgFilterRules.dat file is in your profile, and profile contents are hidden by default, so you'll need to enable viewing of hidden files.

https://support.mozilla.org/en-US/kb/profiles-where-thunderbird-stores-user-data

Do make a backup of your msgFilterRules.dat file before editing it. The results can be unpredictable if such files are improperly formatted. A bad settings file can stop Thunderbird from starting.

Thank you Zenos. I found the msgFilterRules.dat for the specific account. When I look in the file with a text editor, the problem rule is not present - all the other rules I see in the Message Filter dialog are there, but not the problem rule. I can exits Thunderbird, remove the msgFilterRules.dat, restart Thunderbird, and see that there are now NO message filter rules for this account. However as soon as I create a new rule (to begin rebuilding the rules I want), the offending rule reappears.

Is there any other place Thunderbird stores rules or any other way Thunderbird can add a rule to a set of message filter rules?

what is the filter that comes back? We doi have an automatically generated filter that is created when the option to trust mail headers set by spamassasin is sat in the account settings.

Matt said

what is the filter that comes back? We doi have an automatically generated filter that is created when the option to trust mail headers set by spamassasin is sat in the account settings.

This was the answer. I did not realize that if this feature was turned on that a rule actually appears in the Filter list for it.