The world(s) isn't saving properly when you shut the server down (works fine when you just restart), according to console it does save the world(s) but in reality, its like spigot isn't writing the data to disk (Region files). I tested this by placing four blocks where I was standing, I restarted first blocks where still there, shut the server down and went back online the blocks where gone as well as a revert of roughly twelve hours back. Not sure if anyone else had this issue or if it was just me being very unlucky, I reported this to my host as well (McProHosting) and they said it was nothing on their side with restart/shutdown scripts e.t.c and according to console it seemed to have saved just fine. I have log files of this if you really want them but they aren't gonna tell you anything useful since it clearly states the server saves the world(s) every time according to the console. Not sure if you can replicate this error or if I was just really unlucky with having this issue. Awesome work on 1.13 so far, can't wait for it to become a bit more stable and out of early development keep up the good work.