Changing the contents of the script / function while it is running will not affect the script, since MATLAB runs the (generally) "cached" and "pre-processed" version of the file. As for running a script with multiple parameters in a cluster, I assume you are using the Parallel Computing Toolbox ?
One option would be for the script to load its parameters from the MAT file, allowing you to run the same script for all workers, but work with different parameters.
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