So, back in February, I did the flip key conversion for the key fob and as I finished I hit a couple of the buttons and there was a strange beep from the car. Thinking that I had tried to use the remote lowering function (JAGWRANGLER) that I previously installed I noticed nothing happened so I sat in the car and tried the top down button. The rear windows went down but nothing else happened.
After several months of trying to diagnose the problem with several hard resets, no progress had been made. I then got my DMV renewal notice and need for smog test. Car then failed smog test because the catalyst monitor was not ready. Drove it for couple hundred miles and still would not reset.
Took it to dealer and for $215 (1 hr min charge), they drove the proscribed drive cycles and got the monitors reset. Passed smog.
I asked them to look at the top and for another $215, they did some quick troubleshooting. But they have no software to interrogate the modules so they just checked some voltages and ground connections and got puzzled by the pressure reducer valve I installed on top of the pump. They could not find anything and wanted more time to look at wiring diagrams. I said no as I have all the wiring diagrams and I have AE software to interrogate the modules.
Drove car home and as I was grabbing the key fob again to get out of the car I heard a strange noise similar to what I heard in February. So I thought what the hell and tried the top and it works.

Anyone know of any fob button sequence that puts the SLM to sleep?

 

I cannot say I have seen that scenario before.

Check your pump fluid level. Even if it is slightly low, it can cause the top to stall, and temperature can change the level slightly due to expansion/contraction.

One thing I would suggest also: If the top fails to work from either the remote, or the internal buttons, and the fluid level is correct, put it down manually per the instructions in the owner's manual. Then try to operate it again (do not forget to turn the bolt on the pump back to automatic). Dropping the top manually resets the convertible top logic (this is the case with or without the remote top).