MFC will handle this fine, the only problem I could see is from a user(s) point of view is MDI the best choice?

From what I can understand you have data that is related, for example the dialog data and its notes; however in a MDI application this relationship is not that easy to portray without a modal state and can easily become confusing to the user.

I would consider the validity of the MDI approach over a SDI version that swaps the views in or out either by a selection view/menu option or tabs. Microsoft Outlook is a good example of this technique and can be easily implemented through the MFC doc/view architecture.

HTH
Neil