Your sources for apt-get are stored in /etc/apt/sources.list
, so if you really just want to remove a source, you can edit that file and remove the appropriate lines.
However, do you still have virtualbox installed? If you do, you will probably need to put the correct info into sources.list. From virtualbox's website:
Debian-based Linux distributions
Add one of the following lines according to your distribution to your /etc/apt/sources.list:
deb http://download.virtualbox.org/virtualbox/debian trusty contrib
deb http://download.virtualbox.org/virtualbox/debian saucy contrib
deb http://download.virtualbox.org/virtualbox/debian raring contrib
deb http://download.virtualbox.org/virtualbox/debian quantal contrib
deb http://download.virtualbox.org/virtualbox/debian precise contrib
deb http://download.virtualbox.org/virtualbox/debian lucid contrib non-free
deb http://download.virtualbox.org/virtualbox/debian wheezy contrib
deb http://download.virtualbox.org/virtualbox/debian squeeze contrib non-free
So perhaps try changing the virtualbox lines in /etc/apt/sources.list
to one of those lines above (choose the lines which matches your version of ubuntu).