I went to use the Flying Fox zipline today and it was a great experience. It was a great fun.
So, to answer my question - the guy next to the ticket counter will tell you that it's not possible to use only one line but that is in fact wrong.
Once you buy your fort ticket, just head straight through the first gate and instead of going left to the fort, go right and down to Chokelao garden, where Flying fox office is. At entrance to the garden, an officer will ask you to pay 30 rupees for it but don't fall for it. I was surprised at how many people actually pay him. You may enter these gardens free of charge.
One zip costs 200 rupees and it doesn't take 30 minutes as quoted at their website but takes rather some 20 seconds. After a short practice run just below the office, you go to line 1 and are back to the office in a couple of minutes.
A better option is to go for a complete run (I wouldn't call it a tour though). It consists of 6 zips and takes around 30 to 40 minutes to finish (not 1.5 hours as advertised). Zip 6 was my favorite one since it's the longest. I was irritated by spinning while on the line but perhaps that was a mistake on my side.
Runs start at 9:00, 10:00, 11:00, 14:30 and 16:30 but you can ask them to start earlier and they will most probably say it's OK. They did for me.
You can use your video camera either during your run or you can ask the guys to film you from any of the stops. I don't recommend filming during the runs at zips 2-6 since they're longer and you need a bit more control and you don't need a camcorder to distract you. Film the run at zip 1 and ask the guys to film you during the other ones. Bring your own cord for the video camera in case you drop it.
Tip the guys afterward as they're really fun and enjoy their job and you can feel it. BTW, if you get thirsty, you can buy water there as well (and it's cheaper than elsewhere inside the fort).