You will have to make new groups, but it's so easy to do with your new low poly retopo-ed mesh... As for seams, you mean uv map, right?? You make a new map... But see, when you know you're going to retop a mesh, you wouldn't bother setting up the UVs on the 1st one I begin with... So it's not like it's double the work. Now I happened to like zbrushes auto uv method, and then I like to go into Maya and tweek and edit this auto setup with mayas uv tools (more control). If you mean something else by "seams" you let me know.

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