The next version will have a pref setting that will let users choose if they want to remove the glyph name from font.groups and font.kerning when a glyph is being deleted.

RoboFont will not remove the glyph name from the feature file (not in the kern feature or in feature groups)

And subsetting is easier the other way around, I think. Create a new documents and copy all the necessary glyphs from a “master” UFO. (bests with a script off course)

it will remove the glyph name from all groups in font.groups
and it will remove the kerning pair of one of two is equal to the removed glyph

so when a user removes glyph ‘A’

it will remove (if those settings are enabled):
font.kerning[(‘A’, ‘V’)]
and
font.kerning[(‘A’, ‘myKerningGroups’)]
and
font.kerning[(‘V’, ‘A’)]