If the waterproof coating/membrane has been damaged or abraded, no repair is possible. The outer fabric, and perhaps the inner blue/grey scrim offer no waterproofness at all and will let the water through. The best you can hope for is a wash in or spray on reproofer, which will slow the rate of water getting through the fabrics. However, the back of the knee is subject to a lot of wear and flexing in cycling, so any reproofing would only last a matter of a few miles.
The only possible good news is that reproofing the front of the trouses may encourage the rain to run off the thighs more easily, so not much may get to the back of the knees. However, this is probably just optimistic thinking.