I do typically have multiple Emacs processes running simultaneously, but I'm not aware that I kill Emacs processes, I either quit Emacs with C-x C-c, or I click on the "X" in the top right of the window.  Could the latter be sending a kill signal?  By the way, I've exited Emacs by clicking the "X" for years, but I've only recently noticed the warnings.  Also, if I switch to using the version of Org Mode that comes with the distribution (Kubuntu 22.04), instead of using the recent one from a git clone, I don't think I get the warmings.