I will first say that I do not reload any fireformed cases, but I am curious if anyone marks their modified cases to differentiate them from the factory headstamped markings. A friend of mine uses a punch to put a dimple in the head. I've seen this discussed on other forums, but never here. I hope to learn something new with this question.

I'm not sure I understand your question. What's the difference between a fired Hornady 6.5 Creedmoor factory piece of brass from a fired piece of brass from a hand load?

I didn't do a good job explaining. My question is if someone takes a 30-06 and blows it out to a 30-06AI or makes a 260Rem out of a 243. Does anyone mark their cases, so not to get them mixed with the factory stamped cases. I am sure you make lots of specialty cartridges from stamped parent cartridges. Do you mark them so the client can keep them separated?

Typically, shooters who have something specific like an Ackley Improved round, it's easy to identify those visually. Often times I have an ammo box that contains the specific round I'm shooting. For example, I have a 300 Win Mag and 7mm/300 Win Mag rifles. Both shoot Norma brass and both look similar visually. But I keep the 7mm/300WM brass in it's own 100 round ammo box only. So there's no mixing of brass. I process the brass all at once without mixing something similar into it. (I may tumble clean some 7mm/300WM and 308 Win together, but those easily differ visually.)

When shooting or reloading, it's good practice to keep your each individual cartridges together. I don't mix them.

I have seen guys put a Sharpie mark on their cases to identify them. But once you clean them, that marks goes away.

I have not. The only one I’ve done is 35 Whelen to 338-06. I had many 35s though so I put them in a separate drawer bagged and tagged after I had converted everything I wanted to .338. If I had both calibers, the original and the conversion, I would have to find a different method.

No, .223 A.I. and .223 look very different. 7mm-08 A.I. and 7mm-08 look very different.

I can see the difference in 7mm-08 versus .308, and have necked down. 308 before.

However, when I buy 100 pieces of brass, I buy two MTM Case Gaurd boxes, with the real hinge. And then, those boxes get a label maker label on them telling me what belongs inside. That brass lives its' whole life being returned to that laveled box. So I may have 10 boxes on the shelf, all green. I just need to look at the label to know what cartridge is inside.

Marking brass is for match shooting. When over 50% of the field is running the same cartridge, guys get pretty creative marking their brass, usually in the rim, and/or on the case head. "My brass has a blue line in the rim and a blue line on the case head" type of statement. One time I saw a knowledgable shooter/handloader having stuck case problems, and I helped him get them out. Of course I asked if he bumped the shoulders, and he had. Later he told me the brass that was sticking had a black Sharpie line down the length of it. It was puzzling for both of us why only that would stick cases, but it did.

No, the most alike I have are 22-243 and 243 which I have since sold. Always just used Lapua cases for the 22-243 and other brass for the 243.

Loaded up some 6.5X57 and had 257 Roberts and 7X57 ammo and guns at the house at the time. I just made dang sure the keep the 6.5X57 brass made from 257 Roberts separate as only .007 icnch in bullet diameter is not that easy to see the difference at a glance.

I have used color coding of my test loads, marking the primers with green, blue, brown, black or red plus keeping a label with each color, date loaded, grains, bullet, etc taped to my shell box for many years. I also mark the bullets accordingly, so they leave colored marks on the targets. I keep my brass separated, but I have been curious about the precautions others take when dealing with brass cases that no longer match the headstamp.

I pretty much do what has been mentioned above but every once in a while a round or hull from a hunting excursion gets left in a pocket or gun case and I have to drag out a caliper to make sure what I have.

Rounds like 6mm/223 are easily confused but fortunately won’t chamber in a 223 or at least my loads won’t.
Back when I was making 6mm Creedmoor and 22 Creedmoor all from 6.5 Creedmoor as that’s all there was I had to make dang sure it all got into the right ammo box.
Back years ago when I had a 25-06 I don’t think it ever saw anything but once fired 30-06 brass I got from all my compadres that shot 06’s that I downsized.