I've noticed that there are numerous accolades that are tied to nothing more than completing a certain mission.

For example I did a story mission in Romulan space last night with a lower level alt and got Borgification and Hand in the Cookie Jar simply by completing the mission. My main Admiral level character has done every mission available to him and has none of these Story Accolades.

Are these going to be rewarded retro-actively? Or do I seriously need to go back and play every single mission with my max level character?

I would imagine it would be easy to automatically reward these since all you have to do is see if the contact can offer the mission and if they can't then that character obviously must have done it already.

I'm not asking for sub-rewards to be given like find X people in this or that mission (SS Azura, Kuvah magh, etc) just the ones that only come from simply completing the mission...

Also, any eta on fixing the busted ones? I know I saved everyone on the Azura and the accolade says I did but it's still counting as incomplete. Also, I'm sure there's one for saving all the injured people on the planet where you first meet miral paris but I have no counter or complete accolade for that and I rescued most if not all of them.

Even City of Heroes managed to do this with their mission complete badges 5 years ago...

Yeah, I noticed that too. There were many accolades missing from episodic content, Patrol missions, and Exploration missions.

My guess is that the accolades weren't added on until a few weeks after launch, so the first STO player's work didn't get counted. So we have to start over.

Well I know that's not accurate because I was in beta and they were active until about 2 builds before launch. I even got the SS Azura accolade at one point...

They've had these since then and even i they didn't have accolades for later missions in at the time, it's simply a matter of looking at what has already been done via available missions. If the system didn't mark a mission from a certain contact as completed it would still be acquirable and since none of my old missions are re-acquirable that must mean the system knows I've done them which begs the question: Where Are All My Accolades?