Create custom template. Exit limesurvey after editing that template (ie - leave it selected in the template editor). On login and template edit, that template is loaded for editing. That's arguably helpful, though not necessary (and removing that saved setting would also fix the problem).

Not, upgrade LS manually (presumably the comfort update won't have this problem) without saving the uploads folder. Just delete everything and reload config.php (and several other things I've modified, hiding upgrade notifications and so on) by ftp.

Now log back in again, and open the template editor. As the expected (custom) template is gone, the error message will fire without reverting to the default.

Now that I've noticed the custom templates are in uploads, I'll just save a copy of that along with the modded files under applications. But I imagine I'm not the only one to hit this snag.