It’s pretty unlikely the update process could have changed Explorer HAT Pro in any way. The input and output buffers are just hardware, and fairly robust and simple at that.
I’m confused though- how were you getting any signal at all when connected to Output 1 on Explorer HAT? It’s a ULN2003A buffer chip with darlington transistor pairs, and as such only ever connects the output pin to ground. It can’t function as an input.
At a guess- if you’re asserting Output 1 (WiringPi 22) to HIGH, that will be inverted to LOW by the output buffer, and will be connecting the input pin of your transmitter to the ground plane of the Explorer HAT Pro/Pi. If there’s any noise coupled into that ground plane, then that’s what will get broadcast as your signal.