The fluttering is probably the ICP stablizing as you're decelerating and it causes a little rolling or flutter in the engine RPM which changes its tone. This wouldn't be a big issue to correct.
On your particular files, the converter strategy is left stock so it should be locking at the same point it was before. The only major shifting differences are in the 2-3 and 3-4 upshifts, with minor changes in 1-2, 2-1, 3-2, and 4-3 shifts, and they shouldn't be enough to affect the converter strategy.
One thing that might be happening is that because your power output for a given throttle curve has changed, it can have some moderate affects on the shifting because you are using less pedal to make the same power. Since all the major shifts are handled via MPH and Accelerator Position, this can change when and how the shifts occur. I suspect this is probably what you're experiencing.
I hope this helps.
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