Thread:MilkMC/@comment-30539549-20170212011937/@comment-27219153-20170212014239

If players give you coordinates of their chests then, just save those region files.

On the server I run, we are just going to delete the area where the Easterlings are going to be (and save player marked regions if they interfere with the deletion area). Then a month or so after the update we are going to do an entire server reset, excluding player marked regions. Generally, after an update, I think the only part that should be deleted is the part that gets changed, however in our case, the world file is getting quite large which causes several problems (backups taking up much more disk space, backups take longer to unzip (if we need to verify information in them), and backups take much longer to complete). If I played on a server that would delete a player's progress occasionally, it would make my playing experience quite terrible.

I'm sure this is much more than you asked for, but I hope this gives you some insight into how some servers handle this issue.