I got a message similar to that:

"Can't apply upgrade because the following files were modified: template/images/cover-homepage.png, template/images/cover.jpg"

Devin Young, please see Upload Default for Profile Covers.

If it's ok to overwrite modified files, then you can enable the following option:

Studio > Settings > System > SITE SETTINGS > Force site and module auto-update, even if some files were modified

Then try to upgrade again

I keep forgetting about that switch Alex, thank you!