I've learned a few things about video codecs and VirtualDub in general working on Ancient DOS Games. Direct stream copying is only going to be OK so long as you're not chopping that stream up, otherwise it all depends on the codec being used.
And speaking of codecs, after recently updating them I noticed some severe audio lag in my H.264 conversions. The solution was to change a "zero latency" setting, but then, this was for doing H.264 and I'm pretty sure the codec DOSBox records to doesn't have advanced settings like this. One other approach might be to use VirtualDub's audio skew setting in the Audio > Interleaving menu.
One other approach might be to first save the video completely devoid of any audio, since you're replacing it all anyways, then load up the new video and apply your desired audio without making any video changes at all.
--- Kris Asick (Gemini)
--- Pixelmusement Website: www.pixelships.com
--- Ancient DOS Games Webshow: www.pixelships.com/adg