The granting of a long lease is granting ownership of the property under lease, all they actually own is the lease and it will depend on what conditions are in the lease regarding alterations that will decide if they have acted without authority. You should be secure from the Commonhold & leasehold reform act 2002, if there is only one flat with a long lease and the other with an Assured shorthold tenancy. But I would not take precipitous action without checking your legal position.
There is a Leasehold Advisory service in London and this may be a good starting point (telephone 020 7383 9800)