Not sure what clicking is...did he do a mobilization or manipulation on you? Or something else? The best bet is to talk to your physio about the effects and side effects of that treatment.
Stuart McGill is a back researcher that has noted in his book Low Back Disorders, that sitting in one position is often not the best idea even if it is ergonomically correct. Shifting, moving, changing postures, especially if you have to sit for long periods of time, can help reduce repetitive type strain from holding one position.
I'm thinking you have a number of spine extension type exercises (you didn't specify) to help counterbalance all the flexed positions you find yourself in while sitting and on the bike. Definitely keep up with them. You need them. Think of being in flexion as a posture that puts pressure on one side of your disk for long periods of time, which can eventually lead to disc protrusion issues. The extension exercises usually work to put pressure on the other side of the disk, aiding in redistributing the inner disk material to where it originally was, taking the strain off the affected side of the disk. So make extension exercises part of your day and do them often. Consider walking sometimes instead of biking as it puts your spine in extension, so it would be a good change of pace for it.
However, if you have completely different exercises, talk with your physio that did your original and full assessment. They were prescribed to you for a reason. I'm only going by general patterns, as I can't actually assess what is really going on with you. So I'm not getting the full picture.