Help needed combining 3 indesign files into one

[BurkeLand]

I am working on a document that has three sections that are separated into 3 different files. Each has end notes at the end of the document all starting at #1.

There are multiple links throughout each document and I need to set links from one section to the another once combined.

When I use the merge document feature, starting with section one document, when adding section 2 all the endnotes in the "end note text" have reverted to question marks. The reference numbers are fine throughout the document and they do link but the numbers have changed to question marks.

How can I get the three documents into one keeping the end notes intact?

Hope this makes sense and really hope someone can help!!

[Jumpenjax]

Would it be okay to combine them in .pdf? Then you could have control of each page.

[BurkeLand]

What I need to do is set a hyperlink from page 3 of section one to text on page 40 of section 2, so that's why I want them in one document. I'm using text anchor feature for the links.