What might help would be opening the IDML in InDesign CS4 and save a new document from there proceeding with CS6.
But it also might be, that you have no CS4 installed anymore.
I could have a try, if I would have access to your IDML file.
Contact me by personal message and provide a link to the IDML file on Dropbox where I can easily download the IDML file from.
OSX El Capitan 10.11.
And i do not have CS4 installed anymore.
I figured out why some elements were randomly deleted, turns out it wasn't really random at all. When Indesign cut the workspace in half the missing Elements were just placed where there's no workspace anymore, so they won't remain in the document.
And i found a workaround. It's not that time-efficient, but better than nothing.
I made a new document and just copy pasted everything from each page, except from those with missing elements; from those pages i only copied the elements which were left on the half of the page still visible.
Worked, no idea why or how, but i still have to rebuild 9 half pages.
Still would like to know the answer, if not for me, for everyone else who encounters this error.
CS6 is not supported under El Capitan. Some seem to get away with it, but you'd better either reverting your operating system or upgrading to CC2014/2015.
Well, I have no answer exactly why this happened.
You said, that something went wrong by exporting to PDF and that forced the sorry state of your document.
That's a valuable hint. Do you remember an error message in the background process panel?
Or did you cancel exporting to PDF by force quit InDesign?
You could do a bug report to Adobe, but since development stopped on InDesign CS6 and CS6 isn't supported on El Capitan OSX 10.11 it would be fruitless, I think.