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As long as the unique ID of the updated thing your new thing is replacing is still the same (which I hope is the case between updates from ddi - that's the only way things will stay on your character sheet), the replacement will still find the same thing, and HL will ignore it in favor of your new thing. I'm sure the programming of the downloader does its utmost to maintain those unique IDs or is designed to create them in a predicatable way.
You can always create a temp folder within the /data folder, move your creations there, recompile, and see whether the new upload improved anything, and then move the files back after you're done checking.
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