Without the file it is difficult to know precisely what is going on. I 
would say that I do not think it is likely that it is a memory problem, 
at least my experience is that lyx and latex work fine producing books 
with many hundreds of images (tif in the 100MB range), making 
pdfs of 10GBs... :).  But then again, I might have been lucky :)

>! Undefined control sequence.
>l.47 \BOOKM

This is Latex telling you that you have a command \BOOKM 
that it does not know. 

>3. To compile just a part but to tell LyX it should include counter and
>references results in the same error.

I guess this is a good hint. My money would be on that in one of your
references have a included something you shouldn't. :) And then again
this should have been triggered in draft mode as well... Could it be 
something in your file-names or file paths? 

And then again it might me something else, as I said it is difficult
to know without your file. And then I guess you should try, as always,
reproducing the error with the smallest possible file.

Also you could try exporting to latex and run it through latex 
manually, this might give you some more information
as well...


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