Lin,

First remark, which of course you have figured out yourself: the person who 
decided to move from structured to unstructured FM should have his head 
examined (after being fired by the ones even higher in command who no longer 
want to waste their money). The engineers that complain about not being able to 
work in structured FM and preferring unstructured should also be fired, as 
their unstructured attitude will almost certainly lead to crappy product design 
in their own field of work.

That said, there is a way to use structured and unstructured FM in the same 
file and I have succesfully done it. You should NOT use the Ctrl-C and Ctrl-V 
keys as that will bring the content in through the clipboard and as Scott 
mentioned that operation will usually cause all kinds of nasty conversions to 
happen, which you want to avoid.

In my case, the specs for an API was delivered as a set of DITA files, 
generated from the source code by automated scripts (i.e. much the same way 
that you describe your process). The descriptive part of the specs had always 
been in unstrucured FM and is too large and unorganized to be converting 
everything to structured FM or DITA.

The DITA files, saved as structured FM files, were inserted into the 
unstructured FM files as text insets. There were index markers as well as 
cross-references and they all survived this insertion. Also, auto-generation of 
the ToC worked well across the entire file including all the text insets. The 
text insets were not made editable, as that defeats the purpose of generating 
them by an automated process. But they are getting updated automatically when 
the entire book is updated.

Let us know whether this method works for you.

Kind regards from Amsterdam

Jang

JANG Communication
Technical Documentation Specialist
Amsterdam - Netherlands
Cell +31 6 4685 4996
http://www.jang.nl

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