I have 50+ hours in on super good, NCR allying play through, Have Raul and Ed-E as companions. Have joined the BOS just recently and went into the wilderness to hunt deathclaws. Now when I go to any NCR place I get shot at, and my companions kill them for faction fail.

Only thing that could have done this, I was wearing my BOS armor and used it to repair the remnant power armor. The game thought I was still wearing BOS and kept my factions that way. Wearing a powder ganger disguise and taking it off again returned all my reps to normal, but I am still getting attacked on sight by NCR.

Is there any way to reset/clear this issue? I really don't like the idea of abandoning a character with almost 60 hours in due to a game bug.

And my rep with NCR according to pip boy is still Accepted.

you can build your reputation by killing legion members, they say, try it and report back

EDIT: you might just get the dark hero title which means that despite all your killing of NCR, they recognize you sued to do good things for them

also wait a few days before entering an NCR outpost after getting the reputation to dark hero because hostile places will remain suchlike until you wait a few days.

Try putting on an NCR uniform.

If swapping out armor the game forgets to fix factions sometimes. Put the faction armor back on, then remove it. Strip. Don't change into another armor.

Then after you've stripped, then put on the non-faction armor.

I get reputation bugs fairly frequently. I completed the Things That Go Boom quest, went back to the NCR ambassador on the strip, got a reputation boost, became Idolized by the NCR, had an NCR ranger beret on, and then for no reason at all, on my way out of the building, three NCR MPs run at me with cattle prods and attack after telling me "Fancy seeing you outside the strip". I ran outside hoping to get away from them and fast travel somewhere, which was stupid because more MPs attacked me outside and Cass started gunning them all down and my reputation kept going down and down and down and next thing I know the regular troopers are attacking me. I had to re-load a save from 25 minutes previously, before I had completed all the quests. It was really annoying. Not sure why this happened. Never switched armor or anything, just got randomly attacked my NCR MPs while idolized by the NCR and wearing NCR beret.