Can you show us a picture of how everything is wired up? We test these libraries on 328 boards, so that will be best moving forward with troubleshooting.
I have the sda and scl with 5v and ground to the level converter, from there to a pullup resistor to 3.3v (10k, in the orange, though I tried 2 and 5k also), and to the Fast T probe.
The little board is just a piece of soldered breadboard with posts to share the scl and sda among the several probes i will hook up (bar30-which works with this setup, plus later a conductivity probe we are working on) and pullup resistor.
As far as I can tell that looks right, but it’s a bit hard to tell in the picture. I’d verify that the SCL and SDA lines didn’t get switched at some point. Did you ever operate it at 5v without a level converter?
The wires are a bit long and I2C tends to be very sensitive to that. You could try slowing down the I2C bus to reduce the chances of that. Here’s some code to do that on the 328:
// Add these two lines in "setup()" to slow I2C clock to 12.5kHz from 100 kHz
// This is best for long wire lengths to minimize errors
TWBR = 158;
TWSR |= bit (TWPS0);