Alternate layout, table of contents, and bookmarks

[Inélsòre]

I need to export a document in PDF format in several sizes. 

While using a 3rd-party utility that simply rescales the entire PDF, I've noticed that all bookmarks and the table of contents were gone after the conversion. First question here: why is it so? Is there any way around it?

Trying to find a more elaborate solution, I created an Alternate Layout in InDesign.

With Linked Stories, both layouts have a connected ToC. 

Upon exporting the new layout, though, while the bookmarks stay, they are dead (inactive, clicking on them doesn't bring anything). 

I may be missing something very simple but I am not sure. 

Is there anything I can do to perform this action reliably?

The original format is larger than the second one, if this can be of any help.

[Doc Maik]

"First question here: why is it so?" -> This you need to ask the 3rd party tool publisher.

For the actual problem: did you find a solution meanwhile? Your post is three weeks old. If not, could we have an example INDD to test ourselves?

[Inélsòre]

Well, it seems that most applications that offer resizing PDF capabilities (from free tools online to paid PDF editors) strip a document of its bookmarks upon resizing. If they do not erase them, they simply leave them in a broken state. 

The solution I found was to create a new Preflight profile with a new Custom fixup to scale the pages within Acrobat DC. 

I started from here: https://khkonsulting.com/2017/03/scaling-page-content-in-adobe-acrobat-pro-dc/ 

In this way, the document kept its structure intact. There were far more quirks in this process to be careful about than one could have expected but, in the end, it worked. Of course, resizing from 9x12 to 6x8 would result in a perfect match which any non-equal proportion would require carefully choosing the proper scaling option.