You don't mention if the well is water-filled or not.
If you plan to build over the well, it's important that the extension's foundational structure is designed to be self-supporting over the well since it is not made to bear the weight of a building. Even if you fill in the well, the bearing capacity is not completely guaranteed.
It's also important to consider moisture issues if there is water in the well. Even if you fill it in, there will still be liquid at the bottom.
I think you should discuss this with a structural engineer who will need to review the rest of the structure in the extension anyway.