I've lead a change like that - the very core of our data model was compromised from the early days of our company and we knew it... and knew it... and four years into working there I started a serious effort that ended up taking about a year and a half to pay off. These efforts always need a lot of careful planning and you usually want to work within the constraints of early model decisions as much as possible but it is quite possible to gracefully transition. When you're doing something like this it's important to be extremely greedy with SMEs to try and understand as much as you can about the field to future proof your new solution - our company did that once - there's not a chance it'd do it twice.