Long answer: An MSF is necessary to generate your PI Server license activation file. The MSF contains information specific to the licensed machine including hardware, network and operating system information. When you generate your pilicense.dat, it will store the MSF details, and the PI Server will start successfully only if run on the licensed machine. (Source: How to generate a Machine Signature File (MSF))
The PI Data Archive Best Practices article answers your question. The very short version is to regularly backup the scheduled backup directory to a different machine. You can use whatever backup software you like to do so.
