I'm using Affinity Publisher, Windows build 1.10.4.1198.
I'm using XLSX as a data source. It hasn't been changed recently.
Preflight panel shows the warning and a Fix button, but it doesn't seem to work.
I have no idea if my manipulations caused some kind of disconnect. But here are the things I did to create a template:
Initially, I began the whole process in my main document, "Puzzles"
I created a page (not Master) and used the Data Merge Layout tool to create a "Sudoku" grid
After learning more about Data Merge, I decided I should have a separate .AFPUB template
I copy/pasted the page from "Puzzles" to a new document
I belatedly realized that I should be using a Master page
I copy/pasted from the normal page in my new document to Master A
This is key: I was concentrating on the Master page and totally forgot to delete the Data merge Layout from the normal page
The source field on the normal page was called "Solution", then I changed it to "Puzzle" before I copied it to Master A
Meanwhile, I kept tweaking the Master page and renamed the field from "Puzzle" to "N" to help get rid of an Overflowing text frame error
After each tweak, I would save the project as a template.
Every time I generated the merged document and tried to export it to PDF, Preflight complained about three errors
I finally removed the old Data Merge Layout from the normal page. I resized the text frame in the upper cell to handle the Overflowing text error
Maybe all that copying, pasting and renaming confused the software. If not, then perhaps the preflight check is not seeing the XLSX as being unchanged.