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I would like to ask how to properly include the BSD copyright notice within a derivative work (which will not be licensed under BSD).

The original work has a License.txt file attached, stating:
Copyright (c) 2006, The_Developer_Real_Name All rights reserved.

The name of the original work/code is not found on that file and I can see that the BSD template does not ask to specify it either.
I of course know the software name, but I'm bound to the copyright notice that says: "Redistributions in binary form must reproduce the above copyright notice"
So basically, if I'll include the license.txt file as-is, it will imply that my derivative work is also BSD.

So my dumb question is this: how to do it exactly?
What is the common practice to let users/developers understand that the license file refers only to the original work not to my own?
How the users may know what part of the code is BSD and what isn't?

A: 

You can include a file or notification which says "based on source code copyright by the_developer_real_name", along with the rest of the copyright notice. Once you have done this you have acknowledging the source of part of the code, which is the intention of the BSD license with the attribution clause.

If you are not providing source code for your code, there is no requirement under the BSD license that you do so, and you can license your code any way you see fit.

If you are providing source code, provide a license appropriate to your desires, along with attribution to the original code. Distributing a separate copy of the original code along with yours probably isn't a bad idea, even if the build process doesn't compile it.

This is my view based on some discussions and reading. If you care deeply about this, talk to your own lawyer.

janm