Hi Steven,
Node-RED is saving the flow only when you are pushing the deploy button. If I'm right that's the only time you have a write done on the file system. (other than when some Node do it by themselves)
Even with the Pi I had some power problem in the beginning that was leading to the corruption of the filesystem (even if it was an EXT4 with journalisation activated). Maybe it's also what you are experimenting. You should check the kernel log to see if there is any message about this.
Do you have the exact message that Node-RED gave you when you rebooted?
Antoine Aflalo
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