Maybe there should be a system where the company doing the acquisition has to get permission from the acquired company's users before assimilating them... This however is not going to happen since data is so valuable.
For contacts, I have been using a CardDAV server called Davical (OSS). This is supported on iOS and Macs since it implements the CardDAV standard. With 1000+ contacts, it is a more robust solution than scripts for every new phone.
On a similar vein, I also use CalDAV which does the same thing for calendars.