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Worked out the issue through a series of increasingly risky debugging steps!

First I removed the data from /opt/stalwart/data to see if it was a corruption issue. That didn't fix it, so I returned it.
Then I ran sh install.sh again; which did fix it!

I added back the few bits of config that had got wiped (but all data remained) and started to work out what caused it.

Adding the license through the UI was fine. Restarting the systemd service in the command line was fine.

Then I checked the file permissions on config.toml before and after I directly edited it. That was it! The way I was editing it was changing the owner to root. Fixed with a simple...

-rwx------ 1 root stalwart 2070 Oct 24 …

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Answer selected by jamiedumont
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