Nada

I was just confused because in your last post you talked about brushes...
 
Anyways, I hope this helps:
 
Apple Photos
All the photos that are present in the Apple Photos app on your iPad or on your Mac are being saved into the iCloud Photo Library. Of course this only works if you have enough storage space on your iCloud  Drive, which the iCloud Photo Library is a part of, and if you turn on the iCloud Photo Library in Settings > Photos on your iPad and/or in Preferences > iCloud in the Apple Photos app on your Mac. You can check if and which photos are saved in your iCloud Photo Library by going to https://www.icloud.com and sign in with your Apple ID.
 
Here you'll find more information about how the iCloud Photo Library works and here you'll find more about how to use the Apple Photos app on an iPad.
 
Affinity Photo
Photos you edit in Affinity Photo can either be exported to the Apple Photos library or to many other cloud storage services. If I understand you correctly, you are wondering if the photos or projects you store in the Affinity Photo folder within iCloud Drive are being backed up? If that is your question, then the answer is yes! Everything that you put anywhere in your iCloud Drive, no matter if it is in the Affinity Photo folder or anywhere else, will be saved in the cloud and everything is available on all your devices. You can confirm this by going to Settings > Apple ID, iCloud, iTunes & App Store > iCloud > Manage Storage > Affinity Photo on your iPad. 
 
iCloud Backup / TimeMachine
Now, I am not sure if this already answers your question or if you also wonder if the iCloud Backup saves those files again somewhere in the cloud. If that's your question, then the answer is no. The iCloud Backup function does back up everything that is locally stored on your iPad but not anything that is already stored in the cloud. See this article from Apple for clarification what exactly is backed up by iCloud Backup. Apple considers the files in the iCloud Drive already "backed up" because they are safely stored in the cloud already. So no duplicate backup is being produced.
 
The same is true for the TimeMachine on your Mac, by the way. Photos stored in the iCloud Photo Library and files stored in the iCloud Drive will not be backed up by the TimeMachine unless they are stored locally on your Mac. So if you have the option "Optimize Mac Storage" in System Preferences > iCloud > iCloud Drive Options turned on, there's a big chance that some of your files are not stored locally on your Mac, but only in the iCloud. Those files in the cloud won't be backed up to your external drive by the TimeMachine.
 
Does that help?

Is there a way to backup all afphoto files (created with the iPad) in one go from the iPad to another medium? Securing each file individually would be a possibility but is more cumbersome.

Hi DWright...that worked.  Still no idea what happened to cause this issue, but thanks everyone for their help!