I'm having the same issue. Returning player and do not have Story / Datacron achievements for any of my previous characters.
Let me just say that I think the achievements are great. As a completest, I want to earn 100% in each location. If the powers that be are going to retroactively grant us at least the Story achievements... Great! Give us a ETA or at least a guesstimate. Let us know that you are working on it.
If not, then my OCD self runs into 2 dilemmas.
1. Do I continue to play a character and level them knowing that <to me> they will never be "complete".
2. I can't see myself buying or spending Cartel Coins on a character I might have to reroll. (I'm talking the BOE stuff, not legacy)
I hope this gets resolved.