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This is an interesting problem, I wonder if Photoshop or The Gimp actually do something fancy here. There shouldn't be much of a problem replacing files when the files never get bigger and uncompressed ZIPs are used (compressed would make any sense for PNGs and JPGs anyway). Small variations in file size could be compensated with some kind of padding, but it seems to me that we are approaching a point of complexity here, where we should just use another kind of filesystem, one that supports fragmented data.