Switching BLE on/off and get additional 29KB into heap

One way of dealing with this would be that if this setting is changed, the board saves the setting. Then a reboot - is forced - so the system then starts with the new setting?

Yes, that sounds like a good plan.

How about undefining the BLE var ? ... the exception could have a help message?

I'm not sure how we'd do that without modifying the interpreter internals (especially the help message). It's also likely someone may have retained a reference to the function - eg var go = NRF.findDevices.bind(NRF,myFunction).

I don't think it is unreasonable to reboot on a config change if you free up a heap of memory in the process.

Totally - or even just display a message saying Now call ESP32.reboot() for changes to take effect

Just a quick gotcha here: save() saves an image of RAM to flash - if you save a large image and then load it when you have less RAM something will break. You probably want to call jsfRemoveCodeFromFlash whenever you change BLE to avoid this (or you could remove just SAVED_CODE_VARIMAGE - but there's no special function for this AFAIK).