So I beat the game last night and when I returned to the menu I had a New Game+ option and a chapter select option. Then, I unlocked some new costumes and wanted to try them out to I used chapter select and loaded up the hotel lobby in Pittsburgh and saved over my normal save, since that's usually what you do. But now, I not longer have New Game+ or chapter select and the game is treating it as if this is where I am in the game. This needs to be fixed because I want to start my New Game+ and I'm not gonna play through the whole game again from this point just to get m New Game+ option back.
Pick up Load game from main menu, I sure hope you kept your 100% completion save. You can just load it and then both new game plus and chapter select will be avaible again.
I had a weird issue with save files too actually, I finished the game on normal and I had 3 save slots, 2 before finishing and 1 after, next day the 100% completion save file was gone and all 3 showed 97% completion, with different played time tho, I just ignored it and started Survivor that I now finished and so far the save files are there, I deleted the 1.01 update data tho to start new game plus without it as I heard it may be the reason for stuff not carrying over.