Hi Massimo,
The C6655 IOs are not fail-safe and no voltage should be applied if the supply voltage for the IO cell is not present. The I2C might operate for the devices that are powered but you may be damaging the IO cell in the unpowered device. You will have the same issue with all the other IOs connected to the unpowered device. You can isolate the I2C connected to the unpowered C6655 using a PCA9306 I2C level translator. This device has an enable that will separate the two sides. In addition you will be able to connect the pullups for the C6655 to the local DVDD18 for that device. This will ensure that the signals are not pulled up if the device isn't powered.
Regards, Bill