Hi Rick,
You are suggesting that it is to be used as the ebrake signal with R39 replaced by a diode. If you are using the brake lever switches on this line, you are grounding the throttle line which is the same as turning the throttle off. The correct ebrake inputs on the Crystalyte Ver2 controller are HH (switched to +5V to brake) or HL (switched to ground to brake). If the ABS line is grounded, either HH or HL when activated will also activate regen.
It may be that using the term "ebrake" here is a misnomer created by the manufacturer's "Chinglish", with Justin using it initially, but now using the correct term "throttle over-ride."
I initially used the schematic supplied in the CA manual Ver 2, but found it put the controller into an error mode and wouldn't start again without a power down reset. (On seeing your circuit, it was probably just the CA killing the SP line, if I had disconnected it, the controller would have started again). I then tried the version shown in the picture of lazarus2405's article in this thread where the R39 resistor is replaced by a diode between XS+ and the R39's inner pad.
http://www.endless-sphere.com/forums/viewtopic.php?f=2&t=3896#p58220
That gave the same result of stopping the controller. I then set up a small break-out cable to fit between the CA's connector and the controller. A 10K trimpot set up as a reostat was placed in the CA throttle over-ride line. At zero ohms the fault remained. I increased the resistance and found that a measurement where it worked properly without killing the controller was measured at 5416 ohms. I then installed the 5K6 resistor into the throttle over-ride line, removed the break out cable and the problem was gone, the controller worked and the Cycle Analyst did everything as promised. It maybe that the CA settings for ITermMax and ITermMin are wrong for my throttle. It was a generic brand supplied by solarbbq, I don't even know if it's a Hall-effect or potentiometer type. All I know is that it works. Depending on the throttle type, the 5K6 may or not be required. I'll have to investigate this aspect futher.