Dear David
Well, if you are sure you have the roof problem licked and some else will pay for the repair of the floor, and you can find a responsible floor contractor, who will only accept payment when his job is done and invisible, by all mean go ahead and repair the floor now. But be warned sometimes the subfloor has to dry out also (6-9%). This can be achieved if the cupped boards are removed and it is has several weeks to dry out.
In the mean time keep the heat on a little higher, with no nighttime set backs, and heat the basement or crawl space under it well, also. If left on it's own most floors will dry out and settle flat somewhat in a few months. You should be looking for a EMC of about 6-9% in the hardwood and the subfloor, before completing the repair or just sanding. Find out the EMC in your area for indoor wood, from a wood floor mechanic or cabinet maker.
Wood generally will not rot as long as it is in the process of drying, not getting continually wet. But as long as someone else is paying for it, I would choose the first option if I were you.
