Glitch when loading from backup saves

So after defeating the Colossus in the War Room and returning the ichor to the rookery, I selected main hand weapon slot as my upgrade, thinking this would allow me to equip a bow in addition to a sword. I was saddened to learn of my mistake - bows go in the off-hand slot. So I decided to load a save state and select the correct option.

I loaded the Backup from 10 minutes prior and it loaded me back into the middle of the Colossus fight in the War Room, it appears I was missing some healing items but the boss was back at full health.

The big issue, though, is that after defeating the boss a 2nd time and receiving new ichor, I learned that my 2nd main hand weapon slot upgrade had persisted despite loading an earlier save. I went back up to the rookery and unlocked an entirely new upgrade with the new ichor. So I got an upgrade for free and I imagine this could be exploited indefinitely if someone wanted to.