Hummingbird on managed websites

I use Hummingbird to great success on my client’s sites!

When plugins are updated, Hummingbird will pop up a flag recommending running the file check to make sure things are optimized. That’s a good recommendation as files may have been altered, added or deleted.

My question is… Can the file check be run automatically after an update or perhaps periodically? (Maybe a chron job?)

I use icontrolwp.com to maintain my clients’ sites and I can update plugins, themes and WordPress itself without ever visiting the site. Obviously, if I’m not on the site, I can’t see the Hummingbird pop up flag nor run the file optimizer.

So… If Hummingbird is *not* running the file scan after updates, will things be getting messed up?
Thanks!