Hi and Welcome
I'll defer to the experts on pools regarding draining it to repair the area beneath the liner, but in general we don't recommend doing that unless the pool is new - how old is the liner? You could possibly make the situation worse by completely draining it... the liner might shrink and then tear or not line up properly again...the liners lose their elasticity with time and it's not so simple to just do what you describe.
The areas are not something you can live with until the liner needs replacing? Otherwise that might be your only option, a new liner and fix the problem spots.
As for when to convert, I would convert before you close since no one will be swimming anyway. Otherwise you could wait until spring but you would probably have more of a project on your hands if algae takes hold.