Sounds to be a misconfiguration somewhere, virtual machine software can do some weird things at times.
The good is that both your speakers & headphones are working. From what I gather, you desire these to be controlled independent (the norm). You may want to play around with the Sound options, or reset if possible, this would re-enable the default, all sources being independent. Getting there is the tricky part.
Make sure that all of the VirtualBox configuration is removed, you can search for these in the Package Manager. If any VirtualBox setting is checked, uninstall these, all of them, removal of the Windows 7 VM doesn't remove VirtualBox itself. Then run sudo apt autoclean & reboot to see what you come up with. If no progress, may need to install the Pulse Audio package for precise control, although this could be a hassle if frequently switching between headphones & speakers. A reset of the audio components is likely what you need. hopefully others will have a suggestion on how to get there through Linux.
One suggestion may also to reinstall the audio components, codecs, whatever these are termed & hopefully that would solve the issue.......as long as in the future, you steer clear of what caused the troubles. I doubt that drive encryption done this, VirtualBox likely had more to do with the issue. as that was another OS, although virtual, having control over your audio.
Please try the suggestions above, hopefully more will see your Topic & have further input.