passthejoe, 
@killyourfm Thanks for chatting with me on Saturday at the @thunderbird #scale21x booth.
I've been playing around with the folders that are created in Thunderbird from tags in Gmail.
If you have an email with two tags in Gmail, it appears in two folders in Thunderbird.
But if you delete the email from one of the folders, it disappears from the other.
If you want to "remove" from one folder but not the other, the solution I see is to "move" it. (You don't get multiple copies.)