This happened to my guild tonight on HM. We did notice that there were (1), (2), and (3) following the instance name in the Who list when this happened and that our number hand changed to (2) when we had the reset.

I have done everything. The 9th codex entry is for the title. That particular mission just gives you 4300ish credits and 5 vials of the vaccine. No codex, no legacy XP. Possibly regular XP, not sure.

This post: http://www.swtor.com/community/showthread.php?t=414832&page=2 is also talking about this. In there, a CSR suggested to submit a ticket. My ticket was deleted with an email response said it was forwarded to the developers and that I should keep an eye out for future patch notes.