As far as I can tell so far, you can't get TE story after you've taken rio roxo without having gotten story yet. (with the exception of the short arc in Bajatai).
Story can't resume at any old quest - there's specific points in CE+ where it'll resume without another prerequisite quest - but most quests do still also have another quest as prerequisite I think.
"Meet Miguel Mantos" (or something after it) seems so far to be a prereq for all the northern chain of the story; it also seems like it & "An Old Acquaintance" are the only two quests without a quest prereq in TE. So 2 Combat Drones may be all you can get in TE if you skipped story (but you can get those 2 combat drones before you get to FE map at least if doing so).
Update: "Miranda Meets Her Maker" it resumed at it seems. So too late to get the rest of the troops, but in time to have to pay the additional tech. So perhaps a little tricky to get the combat drones while saving a tech.