A simply script to purge a font's groups of any glyphs that aren't in the font anymore.

CleanGroups.py

for f in AllFonts():
    fix = []
    fixed = {}
    todel = []
    for name,contents in f.groups.items():
        for gs in contents:
            if gs not in f.keys():
                fix.append(name)
                
    for n in list(set(fix)):
        cs = tuple([gs for gs in f.groups[n] if gs in f.keys()])
        if cs:
            fixed[n] = cs
        else:
            todel.append(n)
        
    f.groups.update(fixed)
    for gr in todel:
        del f.groups[gr]