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If it exports in pieces it's almost certainly a resources issue, and probably related to some complex placed vector art.
Usual advice in this situation is to do it in pieces and combine in Acrobat.
I manage to combine them in Acrobat X and the links worked, I was happy but for a while. When I tried to save the combined PDF, same thing happened, it just keeps optimizing running at 100.3% of the resources. What I have noticed using my Activity Monitor in Mac is that InDesign renders it using 1GB or Ram while Acrobat only uses 380MB of Ram when I have 8GB of ram available in my Mac. More the reason why InDesign should have gone into 64-bit in CS6, but was dissapointed it did not.
I found the cause of the rendering issue, it is not so much about the vector or image size (it does play a part though), it is because I was using too much Show / Hide functions in the Buttons Panel. There seem to be a limit to how much you can use and on how many pages you can have them. I was doing a "Drop down menu" in the PDF with this particular function, each page have about 40 Show/Hide buttons, and there is a total of 124 pages. That is what caused it not to export out successfully, when I removed the buttons, it worked after waiting for 40 minutes of exporting the file, not very happy it took so long, however it got exported.
I think that both Acrobat and InDesign developers should start looking into able to use Scratch Disk or let the users optimize more Ram to the usage of the software.
Forgot to mention that this only worked in CS6, not even close in CS5.5