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    Have you looked at BTRFS and snapshots? Commented Jun 20, 2021 at 11:05
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    Or ZFS and snapshots. How compressible is the data? ZFS may be able to use your small drive more efficiently. If current is 60GB, how large is update? Is it possible to simply use a larger drive? Commented Jun 20, 2021 at 11:40
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    Going on a bit of a tangent with the 'deployment' aspect - would a blue-green deployment strategy be possible? Having different systems would take away the atomicity requirement, and you can freely switch back and forth between the old and new versions from the network layer. Commented Jun 20, 2021 at 12:36
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    @dirkt This is exactly what I was looking for. It works like a charm for my purpose and I couldn't find a better option. Thanks a lot. Please add your comment as an answer create an answer so that I can set it as the accepted one. Jim L : Regarding the ZFS option, it seems that for licensing concerns it's not as spread as the BTRFS is, I will then go for BTRFS option. Haxiel: It was definitely a very good idea but it doesn't fit my use case (which is an un-networked device). Commented Jun 20, 2021 at 19:19