A local roofer submitted a proposal to me for a roof placement that included replacing rotten plywood with 1/2" CDX. The existing plywood on my roof is only 3/8". I thought perhaps he made a mistake, but no, this is what he is proposing. He said it's only a difference of 1/8" thickness. Is it customary to mix the thickness of existing and new plywood on a roof?
I spent 4 years representing a roofing company in NC. Occasionally I have seen 3/8" plywood on a roof. It is certainly not preferred by professionals interested in quality. Mixing thicknesses is not preferred either, but if you use the proper underlayments and decent shingles, particularly archatectural, you aren't likely to notice. Half inch on a roof is usually OK and very common, at least around here. Obviously 3/4" is better. If you can afford to replace all the plywood, it certainly wouldn't be a bad thing.
If you mix thicknesses of plywood it will cause a problem eventually, and the thicker sheathing will be noticeable (probably within a month)... and this will reduce the life of the shingles, tar paper, and roof. 3/8" should be replaced (optimally) but it would be better to use all the same thickness sheathing than to mix them.
If you absolutely must use different thickness sheathing, replace all of the plywood above the one that needs to be replaced (to the ridge of the roof). In other words, you don't want to have 3/8" above the 1/2" because it will create a ridge that water will settle in.
It's fine, and there is no need for the extreme (and expensive) approaches suggested in some other answers.
Where a 1/2" sheet butts up against a 3/8" sheet, the 3/8" side can have several strips of roofing felt (narrow on the bottom, then progressively wider) applied to ease the transition, before the base layer of felt is applied to the whole roof.
3/8" APA rated sheathing is typically rated for a 24" span (distance between rafters) in a roof application. Half-inch is rated for a 32" span in the same application. Due to market pressures the 1/2" may actually cost less than the 3/8" and will be stronger.