I noticed that some items I had placed in a chest before a scheduled server restart (not the last second, maybe 30 - 60 seconds prior) were missing after the server came back up. The chest was in my claimed base in a non-chunkloaded area. This might have happened before but a lot of the time I wouldn't notice if a few items were missing.
I remember someone else said something similar happened to them when the server was restarted, so I think this might be a recurring, if infrequent, issue.
Not sure who would be responsible for the shutdown code and saving chunks, if it's forge or some mod or minecraft itself.