Setting the center should change the rotation point but will not affect the position of the object. You should be able to modify the center as many times as you want during the course of the script. You can use the node.getCenter command to verify the center is where you expect it to be.
It's a bit difficult to understand the problem without having an example to run. Can you create an example using Vizard's included resources that reproduces the issue and can be run directly?
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