I have found a repeatable bug with linked images in Publisher. Here is the repeat steps.
First create an image in Affinity Photo
Make a new Publisher file, link to the Photo file twice. In each picture frame move to a different part of the image. In Publisher, crop away the part of the image you are not using. In my example I have 4 hats. I crop out all but 1 hat for each "picture frame" in Publisher.
Close the Publisher document.
Edit the Affinity Photo document, save and close
Re-open the Publisher document. The position and crop information has been reset.
Note, that if you do not crop the image this does not happen. But in my case, I am working with a comic book, and I have many images on a single Affinity Photo file. Cropping the images makes it easier to zoom-in and still control the handles of the image. In other words I need to crop to get precise placement.