There are great opportunities to grind Runes very quickly at all stages of the game, so losing some isn’t worth stressing over. If it’s important you get them back, look up a grinding area you’ve unlocked (without realizing it) and spend a few minutes getting them all back and cross that one off the ledger, if you need to. I routinely give up 10-20K souls because you just get so many fighting some of the enemies in the mid-game (or am I late-game? I have no idea…) that I’m not going to run back to a bonfire every time I get close to leveling up. If I lose them sometimes I intentionally don’t run back to them anymore - Runes are a renewable resource. It’s nothing, ultimately.
This morning I was exploring in an area with a lot of powerful enemies AND I had to make some tricky jumps (not really tricky, but you know how it goes, easy to fuck up something you’ve done a couple dozen times without previous issue) and I had over 40K souls on me when I got killed by panic (hidden enemy jumped out at me and I didn’t keep my cool, which is usually how I end up dying to non-bosses). On the way back, I mis timed a jump lost all 40K souls. Doesn’t matter, I can go back to an area I discovered where I can kill (very quickly) 10-12 enemies worth 2.5K each as many times as I care to. I haven’t bothered doing it yet, but just knowing I can makes losing souls feel like not a big deal.