I'm not sure it's the same case, but for those who are in my situation and come across this post, maybe my answer will be useful.
I use Firefox on Windows and was deleting some of my certificates as follows:
Settings → Privacy & Security → Security → View Certificates → Your Certificates
However, when I closed my window and reopened it, they kept coming back...
I didn't understand why until I realized that they were "OS Client Cert Token" certificates.
So I just had to delete them in my Windows certmgr. I deleted it in
User\Personal\Certificates, then the deletion worked in Firefox.