Are you saying you renamed the file? I've never done that and do not know the ramifications of doing so.
Try republishing the file.
You might also want to delete the existing viewer in Viewer Builder and create a new one.
I used a sample1.zip for confirming the Viewer Builder settings.
The sample1.zip is 4pages data of our magazine.
I built a Built-in Single App with sample1.zip by Viewer Builder correctly.
Then the folio of magazine was ready, I published it and exported magazine.zip.
And I just changed from sample1.zip to magazine.zip, but a Built-in Single App is not built correctly with "Signing Failed".
I deleted the App on the list of Viewer Builder and re-built a Built-in Single App again,
the result is same, "Signing Failed".
I changed from magazine.zip to sample1.zip, Built-in Single App is built correctly.
What is wrong with magazine.zip?
I changed Mac OS Language from Korean to English.
Then I built a Built-in Single App with magazine.zip,
developer-viewer.ipa/developer-viewer.zip were downloaded correctly.
Now the status of Apple Approval is "Waiting for Review".
I think there are some problems within Viewer Builder.