Water in Fuel tank!. Now what?

There was heavy rainfall for the past couple weeks in Chennai. Last weekend i made a weekend trip to Coimbatore. Left my bike parked in the office parking lot over the weekend. This turned out to be a bad idea. There was continuous rains for during those two days. When i got back on tuesday, while leaving from office started the bike, everything was fine. No issues on the bike for the first two days, it was riding normally. Then on thursday, noticed that there was noticeable loss of power especially when revving, it was like as if the bike was running out of fuel. But it would'nt stall completely. Problem got worse after a day and i couldnt go over 20kmph yesterday. Took it to a local mech near my house. I initially suspected the airfilter and the spark plug. They were just fine. Then he suspected the CDI ignition coil, blowed compressed air, that did not work. Finally when the carburetor screw was loosened, there was some water flowing out. Still the problem persisted. Then he tried to check if there was a problem with the fuel supply, there seemed to be traces of water when we opened the fuel line, so we drained all the fuel out. Funny thing is that the fuel flow was normal when the fuel tap was in "ON" position, when in "Reserve" it was not freely flowing. Drained the fuel completely and found there was no water in it. Put back the fuel and bleeded the fuel line. Now things were normal again. The Bike was revving as usual, i did notice the RPM was a bit uneven when using steady throttle. Later today was riding it for a while and the problem started happening again. Luckily, a bajaj *** was near by and I managed to ride the bike there. Explained them the problem. They checked the fuel line and there was a little bit of water coming out and the fuel flow was jerky. They told me that the fuel tank, Carburetor and jets need to be cleaned and I can pick up the bike by Monday. Came back home by PTC. Can water get inside fuel tank if parked in rain? This never happened in the past two years almost every time the bike was in the open in my office. If water entered the carburetor, my assumption was that the bike wouldn't even start. How come there was an intermittent issue like this? Have i done any long term damage by riding the bike with water still in the tank?

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