The Remove Duplicate Messages add on to Mozilla Thunderbird does not find all duplicates
As it turns out the duplicates add-on has configuration settings available from:
Tools > Add-on options > Remove Duplicate Messages
From here the different characteristics are choosable for comparison. In my case the two servers stored the messages differently, altering the format of the sender and recipient addresses, the email header information, number of lines, and the total message size. I was able to retain
- Message ID
- Send time
- Subject and
- Folder
and have the search behave accurately.