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The reasoning behind the s106 restriction is to basically stop you from renting out the annex to a third party on a commercial basis or selling the annex on its own. The Council, instead, wish the annex to remain in the same ownership as the property itself, and it should only be occupied by members of your family.
I am not entirely sure what your concern is?
The Restriction is there to stop you renting out the annex (or selling it separately from the main house). Hence, as long as your friend is not paying rent, he would be fine to live there for a short while. If your friend were to live there for a long period of time (over a month) and a third party reported his occupation to the Council , you wold be in breach of the s106 agreement, on the grounds that he is not related and he has a form of tenancy.
So, in short, you have nothing to worry about if he is just stopping there for a short space of time, but if he is going to be there fore a period of over a month, your risk is that a third party reports this to the Council.
I hope this assists and sets out the legal position.
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