Block level deduplication should limit the impact of this case.
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Only if the change is localized to specific blocks.
Besides, block-level dedup is expensive to maintain. Unless you're expecting to find a lot of duplicates -- which probably isn't the case on most end-user devices -- it's a net loss.
Expect about 30%, most of it in smaller system files and libraries. Block-level dedup is great for pretty much anything where you have a consistent workflow.
A consistent workflow sounds like something you’re going to find more regularly on a server than a mobile device or home computer.