hello
where are the files you need to keep? on the directory on your machine ? then you can copy them to ensure they wont be deleted or overwritten
if the files where local somewhere in the vm, try to open virtualbox gui, and start the VM
once done, check over the gui console to login and check if the files are still there, if yes, copy them
vagrant is to create disposable projects, depending on how this is configured, the files may be on the host or the vm
the best is treat the VM as disposable and try to get some persistence on your projects either by copy of the files. or control version.
good luck
alvaro