To fix this issue, stop the server than try deleting all the files other than obviously server.jar, world or what ever the name of your world is, server.properties and the eula text file than restart the server and you should be able to break stuff and no longer have the issue.
I assume it's usercache.json causing the issue but to be sure deleting and letting it recreate the files is a cleaner answer to make sure.
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To fix this issue, stop the server than try deleting all the files other than obviously server.jar, world or what ever the name of your world is, server.properties and the eula text file than restart the server and you should be able to break stuff and no longer have the issue.
I assume it's usercache.json causing the issue but to be sure deleting and letting it recreate the files is a cleaner answer to make sure.