I had the same issue for the last 3 weeks. Story quest disappeared before the Rio Roxo storyline - after Goodbye Commandante. Yesterday i alternately researched tech and conquered provinces to try and resolve the issue. Lol i was tired of waiting for someone to provide a somewhat more helpful answer so i found my own - even registered on the forum just to share the info
My story quest finally came back when I was busy conquering the final Tomorrow era province. I checked for changes in the quests every so often, so it was between conquering the 3rd and 10th sector of Sao Malvado (last province of Tomorrow Map). The story came back on "Miranda meets the maker"
The story was further along than i expected - when looking at the wiki there are about 30 story line quests that i skipped over. So it might turn out that there is a bug, since the story line doesnt make sense if you skip the whole miranda story... but somehow should know that she met the maker
At least they can chance the name of the quest 53 for the people that skip over it
So i think there is a certain set of circumstances that trigger the Rio Roxo bit and if you dont trigger it, it and the whole story of miranda gets skipped. Maybe somewhere along the line those quests will come around - i will update if that should happen.
The problem wasnt tech (even though i went through half the tomorrow era tech tree. Maybe one day when i advance more
For reference, I skipped 2 techs in Progressive and 1 in Industrial... and that gem one right at the beginning. My map has no untaken provinces up to and including tomorrow era