Currently TextSecure (2.0.1) can only import messages from the default Android SMS application once. Afterwards doing the same again results in duplicate messages. It would be nice to be able to deduplicate them.
I assume that going through the list of messages and comparing from, to, time and text would be sufficient. Then just delete everything except the first occurance.
Please excuse me, if this is a duplicate of another issue. It was hard to find good search terms, since “duplicate” occurs extremely often as “duplicate of issue #…”.