Is there any place on the node's file system that is safe from being overwritten during an upgrade? I have some custom configuration that I'd like to not lose during a software upgrade. For now I've been storing it off node, and I'll continue to do that for backup purposes.
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No part of the file system except files containing the submission data (so that configs can be rebuilt from scratch after reboot) and a couple misc files (ssh keys and password files) are retained across an OTA upgrade.
This is by intentional design, a couple of the early beta versions of OTA actually had issues because we retained more than was absolutely necessary to rebuild the node after upgrade. This tight lock down allows the nodes to not be (at least to date and hopefully always in the future) tied to small version upgrades and instead allows major components to be upgrade in the core system without anything breaking.