This can be subdivided into two categories: क़्श and क्श. The क़्श is often written/pronounced as क्श as you likely know. The only two words I can think of with क़्श are नक़्श and नक़्शा, which are both from Arabic. The क्श is present in words borrowed from English, such as rickshaw रिक्शा, action ऐक्शन, etc., and is also found in at least one word borrowed from Sanskrit: दिक्शूल, m. an inauspicious planetary conjunction, &c. (= दिशा-शूल).
Edit: There are many English and Sanskrit origin words with क्श listed here along with a third word that has क़्श (नक़्शी).