Ah, it certainly could be!
I took a look at that thread and dug around our old conversations to see if I could find any additional context, and found this solution that was discussed with the user (not sure how relevant it is to your specific setup, however):
The solution there was to make a trivial change to the affected apps in dev on a new branch, merge into the main branch, and let Protected App sync propagate the changes to the higher environments.
The reason being is that we made a change a while ago to resource references and making an edit on these applications will trigger the migrations needed for the resources to be referenced correctly. You should be able to see a resourceName field being added to the query inside of the git diff view after making the change in dev.
Are you able to give this a shot and see if it fixed your resource references? If not, happy to take a closer look and determine what might be causing this issue.
Here are also a few links to relevant docs:
Let me know how it all goes or if you have any other questions!