Do you mean the App or the VDI disk files? THe virtual machines will be safe (always have a backup regardless).
I checked distrowatch for vbox package but it wasn't listed, but the vbox site does have different packages for the different Ubuntu releases. It's a fair bet that the worst case scenarios (so long as the upgrade goes ok) is that you'll remove the previous VBox package and install the newer one instead.
This may not be relevant but I tried update fron 11 to12 on an older machine only to find it was not possible even though it appeared to go through the motions! It failed due to hardware incompatibility and you may need to consider the hardware requirements.
I upgraded my old laptop, which does not support PAE, by downloading and using the 12.04 LTS mini installer. It will download what it needs from the internet, including the non-PAE generic kernal, from the repositories, so everything will be up to date. Just make sure you have a way to connect to the Internet. Depending on your choices during installation it can eat up a lot of your bandwidth allowance. Mind took just over 4GB according to my ISP. I am usually only 100-200 MB a day, except the day I upgraded my Ubuntu.