This is how I understand it, I'm sure people will correct me if I'm wrong.
People are always advised that discounts and offers can be applied retrospectively to bookings already made, but I think this only applies to the USA. Disney UK has a less flexible "package" regime. Generally, we can't pick and choose discounts anyway, you get what you're given at the time you make the booking. Generally, we don't book room-only packages which is where discounts happen, however in my experience there will always be some sort of discount off rack-rate applied anyway, they might say it's an "online booking" discount, or a "winter discount", or a discount for booking park tickets along with the hotel.
With regard to free dining, you can't retrospectively add it. You have to cancel your previous booking and make another one which has the offer. If you phone them to do this, they can make it as transparent as possible but effectively you are booking a new one then cancelling the old one, which implies there must still be the same rooms available otherwise you won't be able to make a new booking. If the cancellation happens first then there is a danger that someone else could book your rooms in that small gap.
No, you won't lose the deposit, they can transfer and apply it to the new booking. However if the new booking doesn't cost more than the old one they will take a £50 charge, this is effectively the cancellation fee.
I suspect that, because there is usuallty a built-in discount to our packages anyway, that's the reason why you can't add free dining on to that package. Because you'd be getting two discounts! As you say, prices will probably rise during the free dining period. They don't rise as such, it's just that the built-in discount is no longer applied.