Was a fix ever found for the soil moisture sensor not retracting? Most of the time, I can't retract the sensors after they've been extended. I tried multiple ways, extending by data transmission, extending through soil moisture scan, the "toggle" button, but I haven't found any way to reliably be able to retract after extending. Sometimes if I try transmitting after failing to get the sensor to retract, it will jump from the extended loop to the extending animation before transmitting.
I'm doing a one-ship science tour of the solar system, with a mothership that has 2 probes, each including a soil moisture sensor. They start out docked and I redock them from time to time. The only pattern I think I see is that when the probes are out (undocked), retracting is more likely to work, but when both are docked in the mothership, retracting almost never works. Maybe 2 sensors on the same vessel can interfere? Of the few times they do retract, it's often after a significant delay.
Using 1.3.11 with KSP 1.3.0