diff --git a/scripts/inner_source_chroot_update.sh b/scripts/inner_source_chroot_update.sh
index 84e3462..55bccf0 100755
--- a/scripts/inner_source_chroot_update.sh
+++ b/scripts/inner_source_chroot_update.sh
@@ -87,6 +87,7 @@ rm -rf /var/lib/entropy/client/packages
 
 # Make sure that systemd is still the default init system
 eselect init set systemd
+rm -f /run/.eselect-init.run
 
 # copy Portage config from sabayonlinux.org entropy repo to system
 for conf in package.mask package.unmask package.keywords make.conf package.use; do