I have a solution to this problem!
A few years ago I designed and typeset a thousand page, twenty chapter book in Quark 6. I had all the chapters as seperate projects, that were held together in a Quark 'Book'. I was horrified when I found that I could not print all the chapters into a single Postscript file ,with the aim of converting it to PDF in Adobe Acrobat distiller. The book was due to go to print, and I thought I was finished!
The solution is to use a postcript concatenation (joining) utilty called Rundirex.txt (Google rundirex.ps concatenation ps postscript to find more info). Rundirex.txt is a short text utilty that makes the Acrobat distiller gather together your selected separate postscript chapters.
Here is a step by step instruction:
1) Export your quark chapters by 'printing to file' as very high typesetting quality postscript (.ps) files. (I believe that I used the Adobe Poscript Print Driver).
2) Find the rundirex.txt file in your Adobe Acrobat distiller Extras folder. (On my windows system it is in Program files/Adobe/Acrobat8.0/Acrobat/Xtras/). Probably best to search your Acrobat directory.
3) Once all the chapters are printed to .ps format, open the rundirex.txt file in a text editor, and alter the sample paths and files to your needs. This should be self explanatory. My rundirex.txt file had a list of my 20 .ps chapter files, as well as the path to their directory on the hard disc.
4) Rename rundirex.txt to rundirex.ps. Open the altered rundirex.ps with Acrobat Distiller, and the rest is very easy. The PDF settings can be set to your needs. Also, certain page ranges can be selected - this was very useful when my printer could not read more than a few hundred pages at a time, so I split the 1000 page book into three PDFs.
5) Make sure you back-up your rundirex.ps file before you run it.
Please bear in mind this was the workaround used in Quark 6. Possibly, Quark now has decent PDF export options, but this method ensures that full control of the quality is maintained. It also saved me !