How to mark pins that were once extracted on a chain? Like many cyclists, I rotate a set of chains (two chains every 1000 km in my case) to minimise gear wear and have an opportunity to do a deep chain wash every now and then. When the time comes, I replace both chains and the cassette, and the chainrings every second time.

This pattern results in a good lifetime for the transmission, but it means each chain is removed and placed back many times.

The chains I use (HG93) don't have a special connector link.

For safety, it's not good to extract the same regular pin more than once.

So what is the best way to mark the pins that were once extracted?

A very close inspection can identify them by some flashing and scratches, but this is slow and tedious, and never reliable. Sometimes I mark the extracted pins (or whole links) with the etch primer (other paints may not last through the use and wash cycles), but I don't always have it at hand.

What other simple methods do you use or know?
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.