I never use the question index, so I don't really know if the questions/Question groups will disappear form the question index this way, but definitely NOT in the reports. Reports will show all questions, answered or not.
First of all, it would be important to know who is using this form and what it is used for, because this sounds strange:
The reason for this, is not every assessed customer will need all the areas in the survey. Some of them(most of them) yes, but some of them will use only a few of the survey groups.
So are the customers the ones that are being "assessed" or are they the ones that are "assessing"?
Actually I don't really need to know that, but I need to know: Who is filling in the form? The client? If so: how to do send the questionnaire to the client? Do you use tokens?
In the case of tokens, and if you know which client should see which questions, you could save this information in custom variables of the token table and then according to this, hide and show the question groups/questions accordingly through relevance equations.
If you do NOT know which groups the client should see beforehand, you could create a first question with a list of the question groups, where the client chooses from which groups they would like to answer. Then based on this question you can show/hide the following question groups via relevance equations.