Problems with green TWI (I2C) port on Arduino Braccio Shield
I fear we have a colloring issue. Your green is my blue ;-).
I have looked into the data sheet of the level shifter IC and TI only describes scenarios with a higher voltage on the right side and a lower voltage on the left side. Also the allowed voltage translations do not contain 5V to 5V. So I would say in equal voltage scenario the Level shifter may not work.
Answers

Q1: The TWI port is always used with 5V (not ~3V). The Arduino that is supposed to use the shield might be a 3.6V version (like a DUE or M0). Perhaps the TWI port is only intended for this use case: A low voltage arduino with a 5V device. I admit: This should be noted in the documentation. So perhaps Braccio shields work outside the specification and may works under normal circumstances. But meanwhile I begin to understand why they are out of busines ;-).

Supplement: the SCL and SCL signals are routed to two pairs of header pins as they are connected to different pins on different Arduinos. On a UNO you can not use A4 and A5 for analog as they are used for I2C for example. Do you use A4 A5 in any way? Or did you connect the second I2C pin pair in the power header when you had used the TWI connector? (rhetoric question ;-) of cause I will change the answer if you give me more information ;-) )

Q2: The 220k resistor is necessary as it limits the current through the chip if VRef1 is lower than VRef2. Removing it with 0 Ohms would be a bad idea. As long as 5V is used on both sides, nothing would happen. But if Vref1 is 3.6Volts, you would waste energy and perhaps the chip would take part at a grill fest.

Q3: Most I2C devices breakout boards already use their own pullup resistors. So lowering the pullups is not the best idea. -&gt; too high current with LOW signals as the devices pull ups and the braccio pull ups are set in parallel.
-- There is a chance, that the resistors are too large for devices that don't use their own pull ups, but at a 100kHz bus speed I don't think, this could cause an issue.


BTW: You do not need to exchange the pull ups, if you insist to try out different values. Just use parallel resistors to lower the resistance (10K || 10K -&gt; 5K) [|| means connected in parallel] (R || Rp -&gt; (R*Rp) / (R+Rp))