Just based upon the history is that, before the props were tuned, one was more efficient than the other. Now they are both close to optimal. As a result, the fuel efficiency at the same throttle, and/or the throttle applied may be different in effect. And, it would only take a small difference to account for a fuel difference. Also, if there is a cross-over valve, and the boat starts to list one way or the other, that could draw fuel to the lower side, making the difference worse vs equalizing it.
Did you get a report with the prop work? Was one way more out of kilter than the other? Or were their pitches sizes off in opposing ways causing opposing corrections, etc?
Also, check your tachs against a phototach and get them calibrated at cruise speed. From there, see how things go. I have little faith in tachs to be super precise, especially when I don't know who calibrated them and when. They could be causing you to throttle differently. And, people do weird stuff. Someone could have intentionally set them off by a little bit so that they could run with the same indicated RPM without having the rapport synchronized and annoying. One just never knows.
Also, I like to apply Occam's Razor to these things. My first bet is that a valve got bumped or moved while people were working in the boat. My second bet is that a vent got clogged and so it is venting via a cross-over and supply so supply and/or return is favoring the other tank when netted out.