After upgrading to Sonoma, I started occasionally (and then repeatedly) noticing warning messages and errors related to cloud files in my laptop and desktop machines in the area that is for iCloud. The specific files aren't important, although they seem to be related to applications (mostly on the phone) that have transient caches.

However, to stop the myriad warnings/errors, I found a new setting in the backups for:

When a dataless ('cloud-only') file is encountered:

With three settings:

• Materialize: pull a copy to the system before continuing (Arq warns this can be time-consuming and data-intensive)
• Report an error: this is the default and puts an error in your logs (and sends an email if you have emails sent on errors)
• Ignore: just ignore this file and don't back it up

At home, where time and bandwidth aren't as important as a clean backup, I selected Materialize and on my laptop, I selected Ignore, since I don't want to slow things down on the road. The most important items to back up from the road are the ones I'm creating or editing there.

With those changes in place, things seem to be working fine.