Galactic Conquest hard mode not available after completing normal mode

It was possible to achieve the last crate while still missing almost 30 keycards. If you went back and did all boss feats for the first four sectors, I think it may be possible to play sector 5 up to the boss and get the crate.

I think claiming the disk might need to be done because it was a requirement for moving on to each sector. At any rate, beating the boss definitely was. The team may be able to check the logs and see whether you actually did defeat the boss.