I've actually been aware of this before release and just didn't think to file it as a bug because I didn't look at it as a well solvable issue. But for completeness sake, it should still be filed.
When we import a Thunderbird profile we copy all the account prefs that make up a chat account. However, for Matrix we would also need the indexedDB store used for encryption, or alternatively we would have to forget the session ID, so we can start with a new encryption key for the device. The easiest way I'm aware of to get back a well behaved Matrix account with encryption is to remove the account and create it fresh.
Since Matrix account data is almost entirely backed up to the server (including a scheme to decrypt messages for devices that are no longer available, in which TB tries to participate), or alternatively TB will by default store unencrypted logs of the encrypted chats, there is very little data loss chance here.
As a side note, I think OTR has similar issues, but I haven't checked.