I traveled four times on an Indian train. First, Anil and I took an overnight train to Aurangabad, and then return back to Hyderabad. A few days later I traveled by myself to Hospet and back (also on overnight trains). All those trips were very pleasant and problem-free. The trains were clean and pretty much on time, the other passengers that shared the carriage with us were quite and respectful, and in general I felt pretty safe. Though, admittedly, I always felt that there was a risk that when I wake up, I might not find part of my luggage...
Imagine that even when the lights were on and everybody was awake, somebody tried to steal Anil's shoes! Anil and I were sitting on side berths and talking, when suddenly Anil stood up and started following a guy that passed next to us. I was totally surprised by that and had no idea what had happened. After Anil came back, he told me that the guy he followed put on his shoes while passing next to us! He did it without even stopping for a second and I am really impressed that Anil noticed it (I didn't).
That experience made me realized that Indian thieves are highly skilled at their profession and that it might be challenging to protect my belongings from them. I decided to sleep with my camera bag on me (which was super-uncomfortable) and I tied all our bags to the hooks under the beds. Also, whenever I heard somebody passing next to me during the night, I made sure to create some noise and movement, to let the potential thief know that I was alert and ready to take an action. In future, I will also consider bringing a small metal chain, or at least a piece of rope, to be able to better tie my luggage to the hooks.