cvidal89, I have multiple Roku devices within the same room each with its own remote paired to it, so that's not the problem. I have had trouble as makaiguy mentioned with trying to get the remote paired in the first place and having to pull the power on one or more Roku devices. My preferred way of pairing is to put the remote in pairing mode (hold the pairing button until the light starts flashing) and then connect the power to the Roku device. Set the remote down or hold it close to the Roku device and unplug the power from any other Roku devices in the area. Also, make sure the batteries are good. More than one time I've had batteries that wouldn't work to get a remote paired, but were fine once it was.
Once you pair a remote to a stick, it shouldn't matter if you remove the batteries, so I'm surprised that once you got the right Roku/remote paired the left stopped working. There may be something else going on like the receiver on the left Roku coincidentally just decided to die or the batteries were on their way out. Those USB cables with the embedded receiver (and make sure you're using that cable) are always suspect.