for what are these files

[Tweaky]

I think you doesn`t need these two file for the help file:
"autoit-docs-v3.3.2.0-src\docs\autoit\english\html\index.htm"
"autoit-docs-v3.3.2.0-src\docs\autoit\english\html\guiref\GUIEvent.htm"

delete it?

Now look at the screenshot:
There are sometimes 2 lines

I think this is so because of "AutoItSetOption.htm". So a line without a description will be added

<td><a href="GUICtrlSendToDummy.htm"><title>Funktion GUICtrlSendToDummy</a></td>
<td>Sendet eine Nachricht an ein Dummy-Control.<br></td>
</tr>
<tr>
<td><a href="AutoItSetOption.htm#GUIEventOptions"></a></td>
<td></td>
</tr>
<tr>

[Tweaky]

2 lines

[Jpm]

index.htm is supposed to be use on the help access thru the Web. Not sure Jon is taking care of it.
For the other issues will be fixed next beta.

[Jpm]

Fixed by revision [5536] in version: 3.3.3.2