Dependency fields on add people page
perhaps the Profile module create a profile per store and then show the right store profile fields on the registration page, if needed to work with your logic you could place specific stores on specific registration paths with Profile2 Registration Path.

EDIT


  What is the best way to fix this? ... big changes like this aren't possible ...


You asked a problem, I offered a solution. My opinion on the best way to fix your problem is to do some re-engineering of your site. If you disagree that's fine -- best of luck on finding a solution to your problem.

Modules such as views bulk operations, Rules, Node Convert are examples of modules which exist to make sweeping changes of a website feasible (although not without coordination on your behalf). What you say isn't possible -- I say is merely difficult.