Although I haven't tried it, you should be able to keep your focus offsets in either the FilterInfo.txt file (for ACP only) or in MaxIm's focus offsets table. If you want the latter, you should still have a FilterInfo.txt file, but in it, set the focus offsets to 0 for all filters. That way, ACP won't refocus for each filter change, and it will let MaxIm do the focus adjustments.