The Answer
Is Vagrant Provision suppose to wipe out all your data?
No. Vagrant should never harm your "data" (i.e., websites, code, etc.).
...now my whole guest box is wiped out. Is this normal?
Yes. Your Vagrant environment (in other words, the guest operating system created in a virtual environment by Vagrant) is volatile, and you should be able to destroy and recreate it at will without having any impact on your working files (because those should be kept in your local, or host, file system).
Explanation
On Vagrant's website, the very first thing they tell you is this:
Create and configure lightweight, reproducible, and portable development environments.
Your development environment allows you to work. You work on your data, in your development work environment. When you are done with your "development work environment," you should be able to delete it freely without affecting your data in the least.
Further, you should be able to send a collaborating developer your Vagrantfile so that they can create the exact same development environment you used to create your data (i.e., write your program, build your website, and so forth). Then, when you provide them with your code, they can use it in an environment identical to the one that your code was created in without having to reconfigure their own setup.
For more details about how your data files (code, working files, etc.) are kept safely in your computer while making them accessible to your guest system created by Vagrant, see my answer to this question.