I had my logo in the header and it looked fine last night, then this morning, there was just a blank thumbnail with a question mark in it. The same thing happened with some of my pictures too but I was able to fix them. I tried just deleting the logo under the Fifth Options, but the blank thumbnail is still showing up.
You have a section General and the header section from the Option panel.
Favicon & Login logo
Header logo & Mobile logo
Besides that, a Theme will never on his own delete a logo or images. I’m hoping that you made a mistake, or missed the above options. If not there is a issue in you’re installation, that needs to be checked out.