Do the 40% of the graphics that are disappearing all use the same master page. 
If so, look there for the culprit.

Look for .ai graphics on your master pages. Replace them with .eps or .pdf 
versions of the graphic. I had been using an .ai logo on my right master page 
and after the 12.03 update the graphics on the body pages of my right pages 
disappeared. It is a bug in this FM update version that Adobe is working to 
solve.

This is all discussed in the Adobe forums and was discussed here recently as a 
result of my troubles.

Thanks,

Craig
A briefer version of this email was sent hours ago to Denis, but since the 
discussion continues.....
____________________________
>> From: d.d...@icpnewtech.com
>> To: framers@lists.frameusers.com
>> Subject: PDF query
>> Date: Fri, 17 Oct 2014 12:31:14 +0000
>>
>>
>> Hi,
>>
>>
>>
>> My name is Denis Daly. I have recently started using FrameMaker.
>>
>>
>>
>> I have had an odd issue today. I saved an individual chapter as a PDF
>> and about 40% of the images were not present. They are available in the
>> ‘Graphics’ folder.
>>
>>
>>
>> I resaved and the same thing happened.
>>
>>
>>
>> I then saved a third time but selected RGB instead of CYMK; all images
>> were present.
>>
>>
>>
>> I am using FM 12 with the recent update installed.
>>
>>
>>
>> Can anyone explain this behaviour, please?
>>
>>
>>
>> Kind regards,
>>
>> Denis Daly
>>
>> Technical Writer
>>
>>
>>
>> [ICPNT Simple Logo White - Small]
>>
>> Kilbrittain, Bandon, Co. Cork,
>> IRELAND<http://www.myloc8ion.com/index.php/maps/find_code8/?code=WLF-17-68G>
>>
>>
>>
>> Mobile: +353 86 3539962
>>
>> Phone: +353 21 2439119/140
>>
>> Fax: +353 21 2380559
>>
>> Info: www.icpnewtech.com<http://www.icpnewtech.com/>
>>
>>
>>
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