For the see image
When you go to file > Save As Other>Optimized PDF, the optimized dialog box will appear and then click on the white box screen choose Discard Object and uncheck the box "Discard bookmarks" and goto "Discard User Data" uncheck all the box and now go to "Clean up" and uncheck the box Discard invalid bookmarks.
It works on me and one thing Optimize PDF with transparency doesn't break the bookmarks.
This has been seen before. I suggest you flatten the transparency when exporting if you want it done.
So I'm assuming the only way to trigger the transparency flattener in InDesign is to export the PDF with Acrobat 4 compatibility? (The option to select a transparency flattening quality is grayed out and unavailable in the advanced tab of the PDF export dialog with any other option).
Then opening the PDF in Acrobat, inside the Optimize PDF dialog we change the compatibility to Adobe 5 and deselect the transparency box before optimizing? (Acrobat won't let you disable transparency if Acrobat 4 compatibility is maintained).
I've followed these steps, and assuming the flattening is actually occurring in InDesign, everything appears to be working fine.
Thanks Phillip for your explanation. Unfortunately, I'd already disable the 'discard bookmarks' options without success.
Transparency is impossible with PDF 1.3 so that must flatten. I guess Adobe might say that keeping live transparency is very important unless compatibility with ancient software is needed so they don't provide a separate control.
Not clear why you would then further optimize to a higher PDF level - what do you want to gain? More generally, what is your aim?
The distributor I'm working with has a list of specific instructions for optimizing PDFs in Acrobat. (I believe much having to do with the system they use to automatically watermark the PDFs after sale). With you, I'm guessing I can perform all the equivalent optimizations in InDesign alone, and that's what I'm exploring now.