There is no other way than to do it in Acrobat Pro, with Create PDF from multiple files.
If all original documents are INDD you can put them in a INDB and export that.
Did you try a Save As to copy the InDesign file and then make modifications to each?
As I understand it, the basic 40 are in both, plus additional content. (I could be wrong!)
Other ideas are:
1. Use the book features with the 40 pages in one chapter.
2. Use Conditional Text for the differing content and keep it in one document.
Will any of these work?
Ah, I've never used a book file(INDB) but yes that might work. Are you saying Create PDF from multiple files might work?
Yes, you're right, the basic 40 is essentially a "chapter" that is repeated in two PDF presentations, and each PDF has additional, unique content or other "chapters". The book idea could be the way to go. I'll have to try some testing. Thanks!
When you create a book, you put chapters, or files into the book. Use the Book panel menu to do continuous numbering across the book, print the entire book, export the entire book to PDF, etc.
If you have more questions about the book feature, it might be best to start a new thread and close this one off.
Start with File > New > Book, though, and create two books.