How to mark pins that were once extracted on a chain?
You're overthinking this

There are 100-114 links in a chain.  Even blind shooting you have a 3.5% chance of getting the same pin twice out of 5 selections on 114 links.  Even if you did get one twice, it should be perfectly happy to be pressed out again.   

Otherwise use a $2 quick link, which are good for several dozen join/parts.  If you use the proper curved pliers, it will be dead-easy to undo.

When I'm out on the road I don't carry the right tool for quicklinks, so I end up using either a length of brake cable inner that is in my toolkit, or some generic leatherman needlenose pliers, which takes a bit of effort.