Recently I travelled with my bicycle by train to Bhubaneswar from Howrah and came back too without any major damage. I will describe two things that intimidate a lot of cyclists like me. First how to pack the bike and second how to book it in the train.
How to pack it
When you travel by Indian Railways the cycle will be loaded in a seperate compartment called the brake van. This job will be done by the railway appointed porters (you don't have to pay for loading or unloading) and they will obviously handle it rough. They might even toss it up on top of a lot of heaped up commercial luggage. While unloading it off the train they might just slide it down carelessly. So in your interest you should pack your bike well but at the same time keeping it free to be moved around (so don't lock it up). That is if you care for your bike.
First take off all the attachments you might have on the bike like the headlight mount, GoPro mount, saddle bag, Garmin mount and bottle cages etc (these are the precise things that are always fixed on my bike).
I got for myself a few styrofoam tubes that came with my bike when it came by post from Bangalore. I also used some narrower tubes of a similar material for the thinner tubes like the chain stay, fork etc. These tubes are available in Chandni market at shops that sell supplies for the refrigeration industry. In the absence of these, you could cut up cardboard boxes used by Amazon. If you are an outsider you could go to a grocery shop and buy the boxes in which they get supplies.
I used robust zip ties that I had bought off Amazon. In their absence you could also use thin jute threads. I used 3M tapes also.
So I covered all the possible exposed tubes like shown in the photograph. You can see I used small sections for the seat stays or the fork because you cannot cover them with one piece of foam pipe.
I covered the seat with extra care. First I put a thin foam cover and taped it up with 3M tapes. Next was a layer of plastic blister cover. This I had at home, possibly came with some packaging from Amazon. These are also available for sale in Canning Street. After this I put a plastic carry bag over all this and tied it to the seat post with a jute thread. This came in useful for sticking the sticker that they give you after you have booked the bike. It is an important sticker as it has a QR code and all the details about where it is going, who it belongs to etc. I rode on this packed seat for a good 10 km while coming back home. I use a Brooks leather saddle.
I probably have iron butts and didn't feel anything.
But before all this I did two very important things. Got a rear derailleur cage fixed to protect the sensitive part. Some know how to take the derailleur off and stick it to the chainstay with adequate cover like I did for the saddle. I don't know how to do this (will learn it one of these days). But I am not sure if I want to do it during a train journey, as the cage looked like a better protection. I would say this is the most important and vulnerable part of the bike that needs protection. Please don't ignore it.
You can ride with a dent but not with a broken derailleur.
I also did something innovative to protect my bar end shifters (my Surly Long Haul Trucker comes with them). They also look very vulnerable to rough handling because they stick out of the handlebar. First I put a small protective piece of foam tube over it and then covered it by pushing a small PET water bottle over it whose head I had scissored off. It sat very snug and never came off the handlebar in the two train journeys to and from Bhubaneswar.
I didn't use any cover for the front brake levers. I might do that during the next ride with some foam cloth. Not that it was damaged but they look a little vulnerable.
I must add that my bike is a very robust steel touring bike from Surly. A thin and light aluminium road bike might be a totally different vulnerability. But those can be put even in a bag.
My bike has a plastic mudguard from SKS Germany. The rear mudguard, I later discovered, has a very small dent where it has got slightly deshaped. It is possible that this happened during the train ride where there was something thin but heavy resting on the mudguard. It is entirely possible that it happened at home in my absence where the bike might have fallen on something. I have no clue and it doesn't really matter as it doesn't affect the ride. But a mudguard is possibly a good cover for the wheels.
My wheels and hubs and cassette were exposed but nothing happened to them.
Once the train journey is done, the foam tubes can be easily carried in a plastic carry bag and attached to the bike, if you want to use them on your return journey. They weigh nothing. I left them at my friend's house while on tour but if I was going to X and would ride to Y from where I would take a train I would carry them with me on the rear rack.
How to Book It
You can transport the bike by long distance train either as an additional carry on luggage (where it travels with you in the same train) for which you need a confirmed seat in the train. Or you can book it as an ordinary parcel to go by train in which you don't necessarily need to go. The railways will deliver it to your destination station from where you have to get it released by showing the documents.
I am describing here the first method. The second is more or less similar except that in Howrah (and perhaps in most other large stations) there is a totally different godown for doing this. The form to fill in might also be different. In a small station like Bhubaneswar there is only one office for all types of bookings.
First, arrive at least four hours before the scheduled departure of your train (that is what they insist upon) with a photocopy of your ticket and an ID like Aadhaar or Voter ID card. Next get the form.
At Howrah Station opposite to the new Metro Station there is a small one-room office with a blue door that issues the form for taking your bike alongwith you in the same train.
Fill up this form to the best of your ability. Write your name, address, train number, station from, station to, description of the item being sent, its weight etc. There are columns for all this. There are many other things written that are unreadable. Ignore them. Declare the price as Rs 10,000 (even if it costs Rs 200,000) but this you write vaguely somewhere (see the pic). I don't know why it is kept so low. Perhaps insurance comes into play or the rate goes up or they might even decline to take it if it is beyond a certain value. The booking clerk told me this and I complied without questioning. It is possible to insure your bike for the ride but I didn't.
You also have to write a self declaration on the form (anywhere basically) that it is your personal and used cycle and has no commercial value. Commercial rates are obviously higher and rules are different.
On top of the form write the PNR number of your ticket and your aadhaar/voter ID number (for foreigners it might be your passport number). Below your signature write your phone number. After this they are supposed to inspect the bike and put a signature and stamp, certifying that all that you have stated is true. In Bhubaneswar they didn't put any rubber stamp. But in Howrah they insisted that it's a major requirement. I am sure commercial transporters misdeclare the weight to pay less.
Next you go to the booking office with your bike and the form. This is next to platform 17 in Howrah. Here the booking clerk will check the form and tell you what all additional information you need to fill in. I got a very cooperative clerk who showed everything.
They will want a copy of the ticket and a copy of your ID alongwith the filled in form to process the booking. An OTP came to my phone at Howrah which the booking clerk needed to complete the process. In Bhubaneswar there wasn't any OTP.
Then they will take the booking amount, which in my case for going to Bhubaneswar was Rs 109, and issue a receipt. This receipt is an important document which you must produce at the time of taking delivery of the bike. Please don't lose it.
They will also issue a sticker that you have to stick to your bike (I did it on the carry bag that was wrapped as a protective cover on my seat). It is a large sticker with a QR code that has all the information about the bike like who the owner is, where it is going etc. The quality of the gum is surprisingly good.
Now, they will ask you to park the bike at a designated place in the godown. In a small station like Bhubaneswar it could be on a part of the open platform. In Bhubaneswar my train was to start at 6 am in the morning. They asked me to complete the booking process the previous evening. I had to leave it on the platform overnight.
Once the QR code sticker is issued it is the Indian Railways' responsibility to load the bike on the train and deliver it to you at the destination station safely. You are not supposed to even touch it until the gate pass is issued at the destination station.
If you want to oversee the actual loading of the bike, go to the godown at least an hour before the scheduled train time. A coolie will come and take your bike to the designated platform. Once the train comes to the station and all the commercial luggage is loaded they will squeeze your bike in. In my case it was hauled up manually and tossed above the heap of other commercial luggage.
This loading happens in a special goods compartment that we call the brake van. It is usually at one end of the train. While coming from Bhubaneswar there were two such brake vans at either end of the train. I think it depends on how much goods are there to be carried in the train on a given date.