golf.py

import sys, os.path
with open(sys.argv[1]) as f, open(sys.argv[2]) as g:
    settings = [x for x in f.read().split('\n')]
    ids = g.read().split()
mode = 0
for i, line in enumerate(settings):
    if line.strip():
        if (mode == 0) and line.startswith('[') and (line.strip('[]') in ids): mode = 1
        if (mode == 1): settings[i] = ';' + settings[i]
    else: mode = 0
fname, fext = os.path.splitext(sys.argv[1])
with open(fname + '_out' + fext, 'w') as f: f.write('\n'.join(settings))