> ... One of my three colonies, which was very prosperous and crowded in July,
> has all but died ... a few uncapped brood that are shriveled on the sides of their
> cells.

The minimal description given is anadequate for anyone to give a valid
diagnosis.  It begins to sound like PMS (which is also the diagnosis in vogue).
Find someone local who can look at your hive and help (state bee inspector or
beekeeping association).

> What is the best way to save the second colony?
Find out definitively what was the demise of your first hive, and if necessary
manage your second hive accordingly.

> is it safe to use the empty hive in the Spring, or do I need to disinfect it
> somehow?
No one can answer this without knowing definitively what was the cause of the
hive's demise.

Aaron Morris - thinking it'd take a crystal ball on this one.