NG+ Progression

I’m replaying the campaign of Gears 5 and I’ve hit a few snags where I need to reload my last checkpoint to progress. The problem is, for example, that I have already collected all the Jack upgrades and stuff. So when I clear a Condor site, it’s not acknowledging that I have it already, and so it won’t let me leave the area. The same is happening with the side story about Lena and the guy she locked up in a station because he was in a pod. I have to imagine I’ll run into the same issues when I get to the desert areas later.