A section 49 application is unlikely to work in this situation as the occupation has not been adverse.
The management company is likely to be the free holder and may be in a position to grant a new lease of the property on the same terms as the previous lease, there would need to be a recital about there having been an agreement for the lease but that the lease was never granted or was lost before being registered. Some other document affirming that the lease was granted may be appropriate either. In any event a conveyancing Barrister should be able to advise. A submission would have to be made to the revenue on the stamp duty if a new document were produced but they are usually sympathetic in such cases. The management company should have copies of the rest of the title bar the certificates of compliance, you may be able to get these from the original architect or you may be able to pay someone else to do them. Finally the bank should pay for all of this but even if they don't the cost is a lot less than having an unsaleable apartment.
Properties can be sold if the deeds have been lost, its just a matter of constructing a plausible explaination for the purchaser and convincing them that no bank holds them as security.