I have never heard of an instance of this happening before. It could be a case where you forgot to apply the changes, so they might not have been saved. What you could try is to apply the changes once more and check to see if the audit logs in the system information dashlet records that your user made changes to the server settings.
I found it in the server.0.1.log file.
2016-10-19 14:28:47 INFO [DiskUsageHandler] Upper usage limit changed to 1503238553600 bytes
The above shows the change I did on 10/19. Now it has gone back to the default of 250GB, but nothing shows in the latest log files.