Correct me if I am wrong, but it sounds like you click on the
Compile button up on the toolbar (or use the generate primary
layout option on the File menu) to create your .chm files.
There is a better way if you want to generate two "flavors"
of help files from the same help environment, and you have used
conditional tags to identify the content to go into each flavor.
Sounds like you are using the conditional tags, so you are half way
there.
On the Project pane, all the way at the bottom, open the
Single Source Layouts menu - you'll see each available type of
output. Right click on the HTML Help option to open the popup menu,
and select New Layout. You can set up a different conditional
statement and any other feature that must be different than your
default layout to generate your second help file. Save the layout,
and then to run it, you can double click on it in the SSL menu.
I run all my output through this menu instead of using the
compile button - I actually create three different systems from one
help project, using three layouts and conditional tags.
HTH!!!