This might be better in the Acrobat forum, but we'll try here first since the source is FrameMaker.
Today I created a PDF in my usual manner with my usual settings. After adding a watermark and making sure the display options were set correctly, I used the Save As Other > Optimized PDF and, again, used my default settings.
Imagine my surprise to see that the bookmarks panel, which had bookmarks in it before I saved as an optimized PDF, has gone blank. No bookmarks. I tried closing and reopening the PDF in case it was just one of those Windows things, but that didn't help.
Microsoft OneDrive and Crowdstrike Windows Sensor are the only reported changes in my Update History since the last time I was able to generate a PDF correctly. They updated this morning.
Yes, I can always not save as an optimized PDF, but even when leaving the graphics uncompressed, my files usually shrink to 1/3 their prior size so I don't really want to not optimize.
I performed an experiment not long ago, using FM 2015.
I had been saving to PDF using Highest Print Quality, which was the default in my setup.
That gave me a filesize for my book of 10,466 KB.
When I changed the quality to Standard Quality, the size was 5,038 KB.
At Smallest File Size Quality, I got 4164 KB.
I was not able to visually distinguish between the qualities of the PDF.
I also found that when I ran the book through a utility that did PDF file compression, the filesize decreased about 83%, and again I did not notice any visual degredation. I think that was starting with the Highest Print Quality setting. Compressing other qualities also significantly reduced filesize with no visual difference.
Note: when I say "compression", I don't mean using .ZIP or something like that. I mean that the output of the compression is still a legal PDF file.
Unfortunately, our graphics noticeably decreased in quality when I allowed Acrobat to compress/downsample them, even though the original graphics are PDF/SVG and Acrobat seems to restrict its downsampling to JPGs.
I rebooted my computer (on the principle of "sometimes Window just needs to restart because Windows") and just regenerated the PDF using the Print Selected Files option instead of standard Save as PDF. The book went through the old distiller instead of the new PDF engine. This time the bookmarks remained. Not sure if it was the reboot of the changed print routine that did it, but I at least have a PDF I can distribute to reviewers.
Edited to add: File size typically drops from 70 Mb or more to about 3 Mb. Which is actually about 5% of its former size, and no, I don't know why I thought 25% .... It's been a long day.
PDF Bookmarks are a document property which can explicitely be selected for deletion when saving as optimized PDF. Check your optimization settings. In current Acrobat Pro versions, check the settings under "Delete objects", bookmarks are there. In older Versions of Acrobat Pro, the bookmarks could be deleted under "User data", either by enabling "comments…" or or "private application data", I don't remember at the moment.
OK, this is weird and frustrating. When I looked at the PDF that had bookmarks in it, it didn't have all of them. Most of them were removed during optimization, and some of the remaining ones weren't actual bookmarks, either, in the sense that you could not click on them in the bookmark panel and jump to the location.
I think I'm just going to have to leave it unoptimized for now while I try to figure out what is going on here.
Updates, if anyone cares:
If I use Save as PDF, the links and the bookmarks all work but the file is huge, as in 190+Mb.
If I then run the Save as Other > Optimize PDF, xref links are sometimes good but more often bad, and most of the bookmarks don't work. The file size reduces to about 7+Mb.
If I change the optimization options to remove invalid links and bookmarks, most of the bookmarks disappear and some of the ones remaining still don't work.
If I use Print Book, all the bookmarks and links work both before and after I use the Save as Other > Optimize PDF.
I'd wonder if I need to reinstall Acrobat, except this is (so far) the only document this is happening with. It does share some files in common with another book, but the other one renders to PDF just fine with working bookmarks and xref links after going through Save As / Optimize.
I'm glad I have a way to get a working PDF, but seriously, this is getting irksome.