The Due has pullup resistors of 1k5 from SDA to 3.3V and from SCL tot 3.3V. The value of 1k5 is a low value, they should have chosen 4k7 or 10k.
When you connect both Arduino boards, it is 1k5 // 1k5 = 750 Ω combined.
The pulldown current is 3.3 V / 750 Ω = 4.4 mA.
The maximum pulldown current for I2C is specified as 3 mA, that is for normal speed (100 kHz ... 400 kHz). I don't know if the Sercom hardware limits the current to 3 mA, probably not.
The second I2C bus is "Wire1".
There were some issues in the past with "Wire1", I hope they are solved.
You could create a define:
// Select the I2C bus
// #define WIRE Wire
#define WIRE Wire1
and then:
WIRE.begin()
WIRE.write()
WIRE.available()
Are you going to fix everything that I mentioned in my previous post ?