What user did you run this as? Was it the same user that you log into the webui as? Can you confirm you never ran it even once as root?
Could be explained if the ownership got changed to root–or other activities were done on server files while that user.
Also a common symptom of running the server as root.
The webui uses memory to try to feed live logs to the user. If you need actual, full logs, you can simply read the file from the shell; it’s in the server’s live directory, e.g., /var/games/minecraft/servers/myservername/logfilename.log. The logs aren’t lost, they’re just no longer shown past a point because, again, loading files in the webui is a memory/disk load even if you’re not reading it actively.
The page stops loading if it loads over 160 lines in 2 seconds, which is also an enormous load on your browser (and often it’ll start bugging out when your desktop runs low on a bloated browser. Anything slower is likely to be more manageable, hence the threshold.