I think that there is some confusion on reader extensions. A person/process applies reader extensions rights to a designed form. If you read an existing form into designer and make a change, that constitutes a new form. The reader extensions process had been done on the input. You have to reader-extend the form with the changed design after you save it from designer.
I would expect that you would NOT get a message like this if you opened the form in Reader.
Think of reader extensions like it was a signature. If you change the underlying document, you invalidate the signature. The message box is alerting you to the fact that the redesign process will remove the reader extension rights and you'll have to do the reader extension process again.