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[RB] The main issue I've had with InDesign is that its output can't be imported into Flare or RoboHelp (as far as I know). So, as someone else mentioned, InDesign may not be a good choice if you need online help. OTOH, FM content can be imported into RoboHelp and Flare, and perhaps into other HATs too (not sure).
A couple of other problems I've had with InD: my graphics tend to become misplaced, even if I anchor them, and I can't get autonumbered figure captions to work. Both of these cause me to spend extra time on final prep work before building PDFs. I never had those problem with FM. Of course, I'm not very skilled with InD, so THAT may be the real issue here :).
Rebecca
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