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Maybe save the data in the SavedVariables file in kind of groups and add a suffix to the group name (like "_PROCESSED") if the data has been processed by your external program.
The next time your addon checks, if the data for this group must be updated, it will only update the group if the "_PROCESSED" is not present at the end of the name (regex check e.g.).
Though this would keep several empty groups in the SavedVariables. But you could easily rename the "_PROCESSED" groups in your SavedVars, by the help of an addon, to force the update of the data again for newer data for your external program.
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