the VE values are an estimate that the ecu makes, because there will be small changes from one motor to another. fuel pressure, inlet and exhaust manifold designs etc. But yes basically you adjust the VE value up or down till it matches your target AFR. Your new ECU should have an auto-tune feature in it which will help speed up the process as well, as you can then tune the map in large blocks. IE, autotune brings a certain cell down to 64% VE from say 80% that was arbitrarily entered at firsr, you then select a whole block around that cell and adjust them all to 64% VE. When the ecu next goes through these cells it will not need to adjust as much/will converge to the correct values more quickly.
It's kinda hard to explain, but if you watch someone do it you will see it is really simple.
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