It turns out that CrashPlan, the cloud backup service, uses the same metadata to determine what to back up. Macworld’s Lex Friedman pointed me to a CrashPlan support article that looks at this, and that shows how to remove the exclusion metadata. To do so, you run the following command in Terminal:
xattr -d com.apple.metadata:com_apple_backup_excludeItem <filename>
The CrashPlan article mentions this in particular to be able to back up VMWare virtual machines, which, oddly, have this attribute set.
After setting the attribute, you can run this command to make sure it’s stuck:
sudo mdfind "com_apple_backup_excludeItem = 'com.apple.backup ...