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I tried the MasterVariable extension to do so, but no result.
Possible use-case could be: move an from dev to qa and set the environement variable the controls links to databases and folders in the front end before reloading.
Check out this extension Object. Might be of help to you.
I not sure that it is possible, more so for the case you have mentioned.
As far as i am aware the script will always supersede the front end changes.