I've done this a few times. Basically, remove the default glyphs (e.g., a, b, c, etc.) from the font window and from the classes, then rename the glyphs that should replace them (e.g., A.smcp, B.smcp, C.smcp, etc.) with the default glyph names (e.g., a, b, c, etc.) using the "Glyph > Rename Glyphs..." command with the option "Rename Glyphs in all Classes" checked. This assumes you are using class-based kerning. (If not, I'm not sure how you could preserve the kerning. There may be a way, but I've never tried.) You'll also need to remove whatever feature code was used previously to make the substitution (e.g., smcp).
There is probably some way to automate this using Python, but I haven't spent enough time investigating the possibility. I'd like to hear about it if it has been done.