Wanted to chime in with same issue, hoping for a BW response.
The in-game FAQ says all missions, Flashpoints, and Operations will be reward retroactively, but no-go. I logged in with all my characters, but the only thing it registered was the acquisition of the companions.
Everything from class missions to datacrons to crew skills are at 0.
I had 5 max level guys when I quit, so I've got a LOT of time invested that I hate to look at as lost, in terms of achievement hunting.