Javascript Variables Reset When Minimized

I think I'm one issue away from being able to consider this plugin
complete.

My plugin uses a couple of variables in the javascript to keep track of
its state (a couple of booleans and a couple of integers). If I have
the sidebar showing or set to autohide, everything works fine. If I
minimize the sidebar to either the deskbar or the floating deskbar and
then maximize it again, my plugin seems to lose all of its state
variables and looks like it does if you just added it.

I say seems to lose its state variable because if the plugin creates a
notification while the sidebar is in floating deskbar mode, I can then
maximize the sidebar and see the same content item in two different
states -- the one in the notification window showing the correct state,
and the one in the sidebar showing the starting state. Can I not rely
on these variables? Should I store transient state information through
options.Get/PutValue?