The freeholder of the property under conversion has the legal right to use this access across your land to get to his rear garden - you admit this in your post.
So, if the upstairs flat is to be rented using a short-term assured tenancy, the landlord (as freeholder) could include the right of access to the rear garden by the upstairs tenants by including it in his tenancy agreement. Nothing you can do about that.
If the upstairs flat is to be sold leasehold (or even as a leasehold flat with a share of the freehold), the current owner can normally legally transfer with the property lease that right of garden access to that flat - if he wants to. It is more likely to occur if the upstairs flat is sold with a share of the freehold, because the whole of the plot's ground area including the garden would normally be included in the share of the freehold.
I say 'normally' because it is just conceivably possible that the easement that entitles the right of access is written in a way to make this difficult/impossible.
The fact that the flat upstairs doesn't have a direct access to this garden from downstairs doesn't change the price of fish, which is probably the real question you are asking.
Smurfchops is, I'm afraid, not correct in believing that this issue is anything to do with Planning Consent. And anyway, if Consent has already been granted ("the flat next door is BEING converted ....") it is far too late to do anything about the Planning Consent now.