Tom:
Around 1981, I have tried (unsuccessfully) to use the Flag 49 (LoBat) as input means for an HP41C. I used a silicon diode in series with the batteries, with a simple switch in parallel with the diode. Opening the switch lowered the batteries voltage by some 0.65 volt, closing it raises the voltage to its normal level again. However, I was unable to reliably cause the flag to respond to such "modulation". Even if I managed to set the flag, then it will only reset when turning the calculator off and on again. While OFF helped with the first part, and the AUTORUN Flag 11 helped starting my program at power on, the lack of a timer means I must be there to press the ON key each time. (BTW, we have no timer on the 42S, indeed).
I am not sure about the 42S case (it may behave a little differently, and its batteries add up to 4.2 V, instead of 6 V), but it may prove very difficult to achieve any decent serial operation in this manner.
In the memories forum, here at the Museum, you may find my article where I comment these expreiences and the more successful tests on using the TONE instruction to deliver square-wave pulse sequences that could work as a OUTPUT signal from my HP41C.
Just as a possibility, would you think about wiring some kind of CMOS analog switches to the keyboard, and so produce "keypresses" from an external device? It should be not very difficult, and GETKEY is a rich instruction, even with timeout detection...
I will not risk my mint HP42S on such experiments...