If you are baking a custom layout, then you are unlikely to be doing so with any modifiers in the stack (especially if you are following Quanon's routine). In which case the eventual walkmesh would be just like any other mesh. The question is what happens when you dump a walkmesh modifier on it, which should be easy enough to test with any pre-existing lightmapped mesh. No need to bake one from scratch.
That's what I needed to hear! Thanks, DP! Okay, so I can rewrite the walkmesh modifier to take the data from the previous material before replacing it with a walk material and store the data somewhere in it.
I think that covers all the possiblities. Or is there any other reason why max would need the information about the lightmap texture after the walkmesh modifier is applied?