TOPIC: About getting ePublisher to ignore files in a generated merged help system.
In our WebWorks 5.0 help (WinXPPro, Framemaker 7.1, ePub 2008.3), we want to use our Framemaker print books as groups for a merged help system. The project option to ignore front and end matter only grayed out our TOC and Index files. We also want to exclude the LOT/LOF/Preface files.
Here is what I was able to gather from others on the topic. My thanks go to all that helped me! 
1. Move the file so the ePublisher Express file can't link (this displays a file location error in the log).
2. Don't use Framemaker books in the ePublisher Express project. We still create print books, plus we need the book format to run spell check on a group of files, so we really didn't want to continue having 2 sets of book files in sync.
3. Set all paragraph/styles used in the file to no output in the Design project. We couldn’t use this option because the Appendix titles used the same Heading tag as the Preface file so there was a conflict.
4. Use the following PageStyle marker method.
In Designer, I created a new Page style called NoFileOutputHelp and set Generated to disabled.
Created a new marker style in the LOF file and the Marker style area called PageStyle. Entered this for the marker text: NoFileOutputHelp. The marker type value is set to ignore.
- Saved and updated my Stationary.
In the LOF file, I put a PageStyle marker with NoFileOutputHelp marker text into an anchored text box outside of the main flow.
- Opened Express, sync'd saved, and generated the project.
TOPIC: See Also Function in PDF
I've heard that WebWorks will be working on functionality that can be used to push the SeeAlso pop-up link content back into the PDF for processing. If you can't wait until then, check out Shlomo's Timesaver/Navigation marker solution: http://www.microtype.com/ImprovePDF07.html
TOPIC: [Error] Messages
See the page I started here: http://wiki.webworks.com/HelpCenter%20Tip/%5BError%5D%20Messages