I created a map in Illustrator CS6 which I exported to pdf. Using Acrobat 11.0.23 I created buttons which show information when the mouse hovers over the button area. If I reopen the PDF in Illustrator CS6 to change something (like the color of an area)and save it again, all the button functions are lost. Is there a method to preserve buttons made in Acrobat when saving in CS6?
Illustrator CS6 has no interactivity functions. When you open the PDF with Illustrator it does not understand any of the interactivity. So, it ignores/dumps that code. It's non-native code to the application (AI) and can't translate the Acrobat code to AI code because there's no matching functionality.
There's no method I am aware of to get Illustrator CS6 to understand, maintain, and support Acrobat 11 interactive settings.
For interactivity design and basic graphic design, InDesign is a better choice, allows for your interactivity design to be native to your source files, and of course supports direct placing of Illustrator files as well, so you can in fact use a hybrid workflow that should get you everything you need, albeit true that you won't be retaining what you did in Acrobat, you will re-create it once, and then it'll be part of your native InDesign source file from therein.
This is preferable as it allows easy one-to-many iteration and publishing.