Thanks for your post @Nike!
As Walt has mentioned above, the reason that the .afphoto files are shown as 'Affinity Publisher file', using the Affinity Publisher icon is due to the Default app set to open .afphoto files on your PC, through Windows settings.
Please right click on an .afphoto file in Windows Explorer and select Open With > Choose Another App. In the dialog that opens, scroll through the list until you see Affinity Photo (or Affinity Photo 2, depending on which version you have installed).
Select the app in the list and then check the 'Always use this app to open .afphoto files' option, now press OK.
You should find this .afphoto now opens in Affinity Photo, and the icons etc are changed to Affinity Photo in Windows Explorer, as expected.
I hope this clears things up
Nike got a reaction from Dan C in File changes format from .afphoto to .afpub without warning