I think there is a bug in iuse.cpp:
if(((mod->item_tags.count("furred")) + (mod->item_tags.count("pocketed")) +
(mod->item_tags.count("leather_padded")) + (mod->item_tags.count("kevlar_padded"))) >= 2){
p->add_msg_if_player(m_info,_("You can't modify this more than twice."));
If you try to directly repair your twice modified clothing with tailor’s kit by first activating tailor’s kit, selecting your modified clothing on “Enhance what?” question, then choosing “Repair clothing” in “How do you want to modify it?” menu, then you’ll get “You can’t modify this more than twice.” message. If you first try to activate tailor’s kit on some other clothing, choose “Repair clothing” and select your modified clothing on “Repair what?” question, then all be ok.
Sorry again for not PR it by myself 'cuz I’m very poor at programming.