If a separation packet has been thrown out, does my Company have to unflag me?

Go to legal defense and discuss your situation. You need to get the flag removed and possibly promoted as if the flag never happened. This will require some push from the outside.

You still will need a med board and your Command will need to setup. The Army needs physically fit soldiers who pass the APFT, so this situation will lead to medical separation

When you have the legal defense advice go back to your company command and make sure the request is reasonable and in line with legal defense.

Hey man your in a Infantry Company with thick skins. Don't worry on the jumping of the Chain of Command bit, they will forget about that in about 4-6 months with all the other problems they have. Trust me there. Sometimes you have to do that to get attention. Hell, way back when I was in the Army....... I had to stand in front of my BN CDR with my Company CO standing right next to me and tell the BN CDR a urine analysis test conducted was all effed up with chain of custody. CO only held a grudge for a few months then it was forgotten and he got his azz chewed out pretty well. Investigation showed I had cause to be concerned. When you don't have proper chain of custody everyone is in danger of a false positive.

My long ago experience with flags in a Infantry company. Again, they have a LOT going on at once and items are forgotten about. You need to keep mentioning to your Squad Leader and ensuring it is getting to the 1SG that you want them to lift the flag ASAP don't rely on people to remember. At that point you should get feedback as if they plan to lift it, are currently attempting to, or they have no intention of lifting it. If they have no intention of lifting it agree you should go to legal defense as others have said. As for missing a promotion, they can fix that later with a promotion waiver if you push that as well or you can attempt the legal defense route mentioned in another post.

I got flagged for being 1 lb overweight at Ft Campbell once. They are really strict on standards there and I guess I ticked off the 1SG. The flag went on right away, I lost that 1 lb the first week. Took them 45 days to lift that damn flag.

I would contact JAG on this and see what legal action you can take to reverse those actions taken against you. Since Brigade cleared you they should have straightend this out.