This question is really for the Printed Documentation forum.
However...
It sounds like you are editing the online TOC each time. The
TOC when you generated the printed documentation the first time
provided the default print layout. However, in the second page of
the wizard you can edit the layout there to something entirely
different. The two are not linked.
Essentially what you have is say five redirects going to one
topic in the online help but in the print output you want the
redirect out and the the one topic printed in those five locations.
That should not be an issue and should only need setting up once.
Take a look at the printed documentation topic on my site and
see if that helps.
Then if you still have problems, confirm my understanding and
we will see what else we can come up with.
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