After having an instanced service definition for s6-rc, subsequent calls to s6-rc-update seem to clobber the instance/ and instances/ subfolders in a way that keeps the instances running, but makes it impossible to control them.
After s6-rc-update, I get error messages like: fatal: unable to open /run/service/agetties/instance/.s6-svscan/lock: No such file or directory fatal: unable to control /run/service/agetties/instance/tty1: No such file or directory Despite the ttys and the s6-svscan still showing up in pstree and the latter's PID being queryable through s6-svstat on /run/service/agetties. s6-svc -r and manually recreating the instances seem to be the only fix.
