I'm afraid that some of us have been confused by
your post in a thread on a similar subject by Beepjuice.
We're always happy to do what we can to solve your
problems but it would be helpful if you would
start your own thread so as not to confuse your
problem with that of the original.
But, back to your situation.
You indicate that yours is a DC layout. There is a
automatic controller for DC reverse loops. You
can check it out here:
Without such you would need to have a separate power
to the isolated section controlled by a Double Pole Double
Throw (DPDT) switch. You would also need to use a
similar switch for your main track. When the loco
reaches the isolated section you would match polarity
using it's switch. When it then nears the main track
you would use the main track switch to again match polarity.
(the automatic controller does this for you)