The I2C communication over the reverse channel will be sent along with the Video Data. In order for the Video Data to be established, the serializer and deserializer must be configured the same. When you change the configuration register on the remote device, the serializer and deserializer will not be configured the same, and therefore, video data and I2C communication will not be possible. Because of this, after change the configuration register, the local device will not receive the NACK from the remote that tells it to pull its I2C lines high.
The way to fix this is to use the local acknowledge option. This will create an acknowledge when the forward channel is not present, and the I2Cs will be pulled high.