If what I'm about to mention is the sort of thing that you are experiencing, it may help.
I use KDE with a bottom panel set to "auto hide" when I'm not using the panel. Sometimes when I change work spaces, the GUI's for programs I have running in the previous work space are no longer visible, and the bottom panel seems to be gone.
AFAIK, since it's a different work space, the GUI's in the previous work space are no longer supposed to be visible, as long as I have them set to be present only in one work space. Sometimes if I just move my mouse down to the bottom panel expecting it to become visible, it does not. AFAIK, that's not right. But if I click on the desktop background in the midst of the screen, I can then move my mouse down to the bottom panel and it's again visible.
If that's not the problem you have, and a possible work around, please let us know what sort of "Desktop Environment", or "Command Environment" you are using, and some additional details, so hopefully someone can help you.