Hi everyone, here's a quick update with my improved workflow in case it's helpful for anyone else:
Allow all files to save to default iPad locations
Save all files using Affinity Designer "save" function
When project is complete, navigate to folder via My Files
Use Select function to select all and move to Dropbox folder
This means I just have to move everything one time instead of once for every image.
It still reduces the file protection/backup functionality of Dropbox, but Apple offers 50 GB of iCloud space for a buck a month, so I just sucked it up and paid them. Annoying, but not as annoying as losing a project when my kid spills juice on my iPad. 50GB goes quick, but if I'm only using for a project or two at a time before moving back to Dropbox, it will hopefully be enough.