I2C / TWI freezing with SDA stuck at LOW
OK, judging from your scope shots:


What you used to have was the standard weak pullup between SDA/SCL and 3.3V.
What you now have is a short on SDA to 2V, and a very, very strong pullup on SCL to 2V.


I would say the RTC SDA and SCL IOs shorted themselves to the supply. The supply was dragged down to ~2V by the short. (I am assuming that the GPIO that you were using for Vin recovered normal operation after you removed RTC).

As to whether it will recur, I can't say. Moisture on a board is never a good thing. It could end up shorting anything, and give you a variety of odd results. 

Excuse me while I reminisce for a moment...when I was an innocent child fresh out of college, I took several weeks worth of data, only to find that it was all useless because my board had iced up. Everything sort of worked to the point where I didn't notice anything until I was actually analyzing the data. My rise time, fall time, and jitter had all gone to hell.