How to combine multiple PDFs with form data WITHOUT flattening pdfs OR changing form names?

We have thousands of forms that need combined into a single PDF. We simply do not have the time to rename all of the forms in each document, or flatten every PDF. Is there a fix for this? All of the information in our forms end up being blank after combining them.

It is extremely odd because my boss was saying this was not an issue before, but it is now.

It never came up with this dialogue box saying the following until today:
"Any form fields that have the same name in the merged documents are now merged into one field. If you want the values in these fields to be unique, then you need to create a PDF portfolio instead of merging the files. To create a PDF Portfolio, choose File > Create PDF Portfolio."

As far as we know, Acrobat didn't update. We really need a fix for this. I was thinking maybe creating a custom action to flatten would help make this process go faster? Or I was reading that there maybe a javascript fix for this to batch flatten them all at the same time?