Users Syncing to Old Home Folders

Two users in my office are suddenly complaining that their machines are syncing again. This doesn't surprise me, because my supervisor told me he had reactivated syncing over the weekend. What surprises me is that the server is re-uploading files that the users had deleted years ago, and taking several hours to do so. To my knowledge, when a machine hasn't synced (or is it sunk?) in a long period of time, an alert will display showing a choice to keep what is on the machine, or what is on the server. But according to the users (one of whom happens to be the president of the company), no such choice appears. The users are able to cancel the home sync and continue along their merry way, but obviously I would rather their current directories sync to the server in case of some mechanical failure (one of which has occurred just last week, causing a separate user to lose all their files, which prompted the reactivation of the syncing in the first place). In this case, the users still have all their current data, (except certain program licenses which will need to be reinstalled,) and multitudes of deprecated data. I'd like to nip this problem in the bud, before my entire office comes running to my desk with the same issue. Any suggestions?