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Does anyone know what method is used by Casper admin to work out which files need to be replicated or not? Is it using rsync under the hood or another method?

by default I think it's modification date or file size. you can change the method in Casper Admin's preferences. I ran into a similar issue recently, the permission on the CasperShare I was synching became corrupt (server.app flub?). Casper Admin reported success even though files were not copied.