I've done it also, when I felt that my previous pre/pro was setting the x-over very high. If you lower the x-over, it will give some overlap in the range where the difference from calibrated is. That range will be uncalibrated, so there is no telling if it will sound good or not. When I switched to my current pre which has Audessey Multi-EQ, the x-over is a bit lower than before, but still higher than I expected. When I listen to it as is now though, I like it and only adjust the sub level for music vs. movies (calibrated for music, +3dB for movies).
I recommend leaving it as is for a while and see if you like it or not before changing it.