I would like to make a backup of the server in case the machine has a problem.
Should I make a copy of the entire database and configurations, install SyncThing on the new machine, and copy everything over the existing file?
Or should I just copy:
config.xml cert.pem key.pem
And overwrite it on the new machine?
Those three files are the most important. Don’t copy the database.
That sounds like you are setting up a new machine that can co-exist with the primary one? In that case, it would be troublesome if both have the same device ID. If you’re just interested in restoring the device ID and config after the old one goes down, then yes, the three files should be enough.
Only back up the database if you are 100 % sure that it will be restored together with the synced folders, exactly as they were at the time the database backup was taken. I certainly recommend against trying that.
No, the two machines won’t have the same ID at the same time. I have a backup machine configured as a client of the main server; it has all the files mirrored. If the main server has a problem, I intend to reconfigure the backup machine as the main one. This was the quickest way I could think of to re-establish the file server. I have a backup in the cloud, but downloading everything will take a while.