Have you tried opening, editing, and saving another file in Affinity? It sounds like you might be having issues with your Affinity installation (I’ve read some recommendations to reinstall affinity from their website using the .exe extension but have not experienced this issue myself.
For missing files, you’ll want to move everything to the same folder (before opening Publisher), open the template, open Resource Manager in the windows drop down, and then update or replace the assets using the new file location (the folder where you moved the assets using).
If you can open and work with other Affinity Publisher docs, you could always copy and paste template content over and save there.
hope this helps!
watt