Actually, I don't think you can hurt much stuff with both 5V and 3.3V fed to the board. The voltage regulator might go up in smoke, but I think the rest is okay so long as the FTDI chip isn't powered up. And even it might be fine.

The VDD_IN pin of the WT32i connects directly to the "3.3V" pin, and that's perfectly safe to do. I'm just not understanding the VDD_CHG and VDD_BAT pins, and what should really be done with those. The datasheet gives a couple of suggestions, but my head hurts and I'm retiring for the night now.

Cheers