If there is a world error at startup, first protect the data and find out which file or region the error occurs in. Don't keep rebooting on the problematic world.
Step by step
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Stop the server and make a copy of the current directory. Keep the last hard backup and note the first file or chunk error in the log.
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Open a separate copy with the same version and world manufacturer settings. If the problem started after a new plugin or Java update, compare the changes.
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If you have a hard backup, restore it in a separate directory and verify the affected area. If you're only considering region repair, try the process on the copy.
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Replacing files with live ones without passing the starting, birth, target coordinates and other dimensions.
Keep in mind
Deleting the region file may also cause loss of player structures in that region.