You can draft your lease in such a way that increases the value of the freehold without inhibiting the sale of any of the flats. There is no point in drafting a lease with 999 years and no ground rent increases. If somebody has drawn up your leases in this way then you need to think about getting somebody else to do them in future.
Selling a flat with a lease of 125 years is pretty standard with ground rents doubling every 25 years. You will have no problems selling the flats and the freehold interest will have some value. It is also beneficial to have the management rights assigned to the landlord or his agent. This is also a good selling point for the freeholders point of view.
Unless there is a very good reason to sell a 999 year lease you should not do it! This is the worst type of lease to sell even if they are favorable ground rent increases. The landlord is never going to get a lease extension and the value of the freehold will only be a fraction of what it could be with 125 year leases