I plan on replacing many bolts this season and would prefer to just remove the old bolts, some of which got chopped and are now rusted pieces of junk, and place the new bolts in the same hole. Is this a big No-No or is it cool? Will I have to make new holes for the bolts, if so should I do it on lead with a hand drill? I have placed, but never replaced, hardware and would like to start making some dangerous climbs safer. Thanks for any input.

Drilling on lead and making "a route safer" are subjective calls, but you should definitely plan on new holes.

I only drill new holes when the old ones are not suitable for a replacement, or I am replacing on lead. When replacing on lead the best bet is to clip the old bolt, hang and drill a new one, then chop and patch the old one. This is not ideal BTW...much better to replace bolts top down.

When selecting to use the old hole I look at the angle the bolt was drilled(is it perpendicular to the rock) and if the new hanger will sit flush where the old bolt was. If the bolts are chopped and there is part of the bolt in the hole I usually drill a new hole unless it is only a sleeve or cone. You can drill a 3/8" stud out with a metal drill bit but this is a lot of extra hardware( bit and chuck)unless you have several to replace. Technically SDS bits will drill through rebar, but you will go through a lot of bits in my experience. You also want to plan to use a larger anchor, ideally both in length and diameter.

Replacing bolts is a lot of work, and getting it right is pretty important. I would really suggest you find someone with experience to walk you through the process the first couple times.

This should answer your questions - http://www.safeclimbing.org/education/howtorebolt.htm.