There used to be a #discardChanges or #forgetChanges or some message like that that allowed one to discard .changes file. But I cannot seem to find that anymore in 5.0. Maybe it is #closeSourceFiles.
The reason could be becuase the do-it (same as executing a .st) are tracked in the changes file. Another possibility is to explicitly disable the announcers, hoping that the changes writing happens via announcements:
SystemAnnouncer uniqueInstance suspendAllWhile: [ self executeYourScript ]
Hope this helps.
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