(I can't find the mega-thread for this so I post this in hopes it gets added to the ongoing issue)
This happens to me on every playthrough I've done since I started playing in May.
At some point between level 200 and 400 I will login, or come out of a shop, or come out of the tattoo shop in Ravensthorpe and one random rune from from 3-5 pieces of my equipped armor.
In my experience it is always + Life Runes, I've never lost a weapon rune in this way. (this has not been a huge issue for me since adding a +18 life rune doesn't actually add +18 life, and never has, it only adds 3-4 life I assume from diminishing returns) Today it was some +14.9 Life runes, in the past it has been either 14.9 or 18.9 life runes.
The armor sets this has happened to include the Mentor's, Druid, and Einherjar from the store in various playthroughs.
I've never been able to capture it happening before until today.
This video shows me logging in a little while ago from a main save game file, finding 3 of my runes disappeared (all life runes). I was able to load in the same game immediately from an autosave a few minutes prior where you can see the runes in place.
The cloud save for this game file is available to grab as well, although it will most likely be the restored version.