First off – ask yourself are you really doing Agile? If you are then you should have already delivered a large portion of usable functionality to the client which satisfied their requirements in the earlier sprints. In theory, the “damage” should be limited to the final sprint where you discovered you needed large design changes. That being the case you should have proven your ability to deliver and now need a dialogue with the client to plan the changes now required.
However given your description I suspect you have fallen into the trap of just developing on a two week cycle without actually delivering into production each time and have a fixed end date in mind for the first proper release. If this is the case then you’re really doing iterative waterfall without the requirements analysis/design up front – a bad place to be usually.
Full waterfall is not necessarily the answer (there’s enough evidence to show what the problems are with it), but some amount of upfront planning and design is generally far preferable in practice to the “pure” Agile ethos of emergent architecture (which fits with a Lean approach actually). Big projects simply cannot hope to achieve a sensible stable architectural foundation if they just start hacking at code and hope it’ll all come good some number of sprints down the line.
In addition to the above another common problem with “pure” Agile is client expectation management. Agile is sold as this wonderful thing that means the client can defer decisions, change their mind and add new requirements as they see fit. HOWEVER that doesn’t mean the end date / budget / effort required remains fixed, but people always seem to miss that part.