We have exported a TM as TMX file from WorldServer and performed some changes in the target translation of some TM entries in Notepadd++. We haven't changed anything else in the TMX file.
When importing the TMX back into the TM, the entries where the translation was changed have been added to the TM. They have not overwritten the existing entries. This behaviour is to be expected, as explained in this article: WorldServer: Is it possible to update TMs without creating duplicates?

Since these TM entries are now both in the TM with the same attributes, including creation date, modified date, entry origin etc,., how will WorldServer decide from which of the two TMs it will leverage from?

Under this scenario, only one attribute will be different: the Import Job ID. The Import Job ID of the last imported TM entries is higher than the one associated with the already existing TM entries.
When everything else is identical (remember that the TM leverage is based on the source text, not on the target), WorldServer will leverage from the TM entry that was imported most recently based on the highest Import Job ID.

Therefore if - for example - the exiting TM entry has Import Job ID 3670 created after the import and the existing one has an Import Job ID of 3669, WorldServer will leverage from the TM entry associated with Import Job ID 3670.

Relevant article:

WorldServer: Is it possible to update TMs without creating duplicates?
Worldserver - How to search for and delete duplicate entries from a Translation Memories?