It's unlikely that SONAR changes the sample rate "for no reason". SONAR in fact cannot change the sample rate at all. It can only make a request to the driver to make a request to the interface to change it. Ultimately, it's the interface that decides the sample rate.
Many interfaces, including my own MOTU, default to 48KHz when they're first turned on. Others default to 44.1KHz. The first time you run some audio software such as SONAR or Windows Media Player, that software will request a sample rate via the interface's driver.
I
think (don't know for sure) that SONAR does this just once, when the project is first loaded. If the sample rate were to be subsequently changed by some other software while SONAR is still loaded, you could end up with an incorrect rate.
Maybe I'm misunderstanding the scenario. When you saying "boot up a 48K file" does that mean opening a 48KHz project, or importing a 48KHz file into a 44.1KHz project?