I am sorry to say I am not sure what level I am actually on, but I will try and describe.
I am back at base after doing 2 (I think) away missions in a row. And I have just bumped into the "New Paradigm". When I left off last night, I could research and build commanders. When I loaded back up this evening I could not.
Please note I am talking about loading from the save point created at the end of a mission, not mid-mission. AFAIK I still have commanders in my mid game save.
When I start this next mission, I have a 2 hour timer, and am about to stumble on bases in the lower right corner of the map. I can research hardpoints and bunkers for the first time. I hoep this is enough info.
Not sure if it is a bug. If it is, vould you please move it to the appropriate forum.