Can error messages be avoided for custom modules in the Update manager?
Using the tip that junedkazi gave (please up-vote his answer too if this helps you!), I add this line to the .module file for my feature module:

include_once('&lt;my_module&gt;.exclude_from_update_list.inc');


And in the file &lt;my_module&gt;.exclude_from_update_list.inc:

&lt;?php
/**
 * @file
 * &lt;my_module&gt;.exclude_from_update_list.inc
 */

/**
 * Implements hook_update_projects_alter().
 */

function &lt;my_module&gt;_update_projects_alter(&amp;$projects) {
  unset($projects['&lt;my_module&gt;']);
}


And it worked perfectly.  I took the precaution of backing up the database first, and of course I did this in a non-production environment.

This is all pretty obvious once you know about that hook, but I'm putting the code here for sake of a more complete reference, hoping it speeds things up for someone else.