Why did my index.htm file generate blank? and other weirdness.

Here's the story. Maybe someone can tell me where I made my mistake, or what happened. I'm numbering the steps for convenience in discussing this.
1) I started a new project, a WebHelp project.
2) I imported content in Word.
3) I created an index, glossary, and TOC. I used wizards for some of this.
4) I created a style sheet and applied it to all the topics.
5) I added a skin from the gallery.
6) I generated output.
Then I sent that output to the UI developer on my project. He plugged it in to the web app, and it seemed to work fine. So then:
7) I opened the project, edited the text, and removed glossary links (because I didn't like how they were working) individually.
8) I generated a new TOC to match the changed topic structure (minor changes).
9) I generated another output.
I sent that output to the UI developer and he said it was blank. I opened index.htm and sure enough, it was indeed blank. In fact, it was Zero KB. I also noticed that four other files were blank: whfform.htm, whform.js, whskin_plist.htm, and whtbar.js.
So then I decided to start over. I created a new project, imported just the html topic files from the old project, redid the index (in a  hasty and less thorough manner), decided to bail on the glossary for now, did a TOC and sent that to the developer.
Now the Search pane is totally wonky, showing a list of characters and terms.
So I am getting frustrated. The developer has tried monkeying around with stuff on his end, but it's not working. So he says, why don't you send me a build with everything?
The problem is, I have two broken builds. The first one, which for whatever reason has the blank index.htm file (and other blank files), and the second one, which has no glossary, a messy index, and a screwed up search.
I can't seem to find anyone else having this problem. :-/  Can someone help? 
Thanks so much,
Tamarleigh

I am having the exact same problem, and I think I've figured out what is happening here. There is an issue when mapping Word styles into RH. The person who setup our Word template included a sidehead with conditional text to hide instructor notes when printing participant training manuals. I removed the conditional text, and everything is working fine. You may want to double check to make sure you don't have conditional text in your Word docs. I've uploaded an image with the code below to show how the conditional text looked when the document was linked and generated.
Check out the code below:
<table cellspacing="0">
          <tr>
                    <td style="vertical-align: top; padding-left: 0px; padding-top: 0px;
                               padding-right: 0px; padding-bottom: 0px;" height="800" width="114"><table
                               cellspacing="0" width="100%">
                              <tr>
                                        <td style="padding-left: 0px; padding-top: 0px; padding-right: 0px;
                                                   padding-bottom: 0px;"><div v:shape="Text_x0020_Box_x0020_146"
                                                                                                                         class="shape" style="padding: 3.6pt 7.2pt 3.6pt 7.2pt;">
                                                  <p class="WD_InstructorNotesHeading"><span style="background: #ffff00;">Instructor
                                                   Notes:</span></p>
                                                  <p class="WD_InstructorNotesText"><span style="background: #ffff00;">Add
                                                   any additional instructor information into this text
                                                   box.&#160;&#160;It will only appear when hidden text
                                                   is turned on.</span></p>
                                                  <p class="WD_InstructorNotesText">&#160;</p>
                                        </div></td>
                              </tr>
                    </table>
                    &#160;</td>
          </tr>
</table>
Cheers.

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