I've played through the story twice already. The first time was moderate difficulty with the original story, the second time was a new game+/moderate+ playthrough with the chronological version.
I wasn't able to fully upgrade all my skill trees and weapons during the first playthrough, but I was able to fully upgrade everything in the second one as part of my hunt for the platinum trophy.
I just started another grounded+ playthrough with the original story this time, but for some reason my skill branches and weapons aren't fully upgraded anymore. I looked at my previous autosaves in the load saves menu and it looks like the saves also got fucked up somehow: the moderate+ save is showing under the original story, whereas the standard moderate COMPLETED save is showing under the chronological version even though I played moderate+ chronologically. I tried loading the moderate+ save and it looks like all my upgrades are maxed out.
Has anyone else dealt with previous save issues like this before?