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Not sure whether or not the repointing affects the clean command, but I think that it removes the last compiled script in the rom.
The best thing is to test it out on a backup rom, (creating a backup and making a short script to test it out) and after compiling and making sure that the script is working in game, next step would be using the clean command and making some changes to the script to see if the offset is the same, and whether or not the script has changed in game.
Once that is successful, you can test out the same thing but with repointing.
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