Database Update Clears My Uploads Folder

Every now and then, I’ll log into WordPress and see a message that a database upgrade is required. (This one.)

The down side of this, is that clicking the button clears my /uploads folder, which means I lose all of the images on my site. Thankfully, I’ve made a local backup of the directory, but this isn’t something I want to deal with on a weekly basis, which is how often this seems to happen.

Any ideas in the community?