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It would be advisable to contact the freeholder to inform them of your plans and let them know that the council will be contacting them to discuss the planning application. The remedy is better than the cure, as breaching your leasehold agreement could lead to the freeholder taking legal action against you.
The freeholder shouldn't unreasonably withhold consent. There is normally a charge involved with obtaining approval, in the form of a License for Alteration.
Also, it is important to note that contacting the freeholder sooner rather than later could prevent delays during the planning permission process.
If you like I am happy to review your draft letter and offer some feedback as a premium service