You did not synchronize the
wrong way. There is no right or wrong way to do so, except if—when offered the choice of merging or replacing data during a first-time synchronization event—you make an inappropriate choice. What occurred is the normal, predictable outcome when you remove data from an application, device or server—or, it is effectively removed by some action other than one you took—and you subsequently synchronize. iSync, and other components of the Sync Services framework, are designed to equate records sets everywhere following a synchronization event.
Read this document to gain a reasonable understanding of how this technology works:
http://developer.apple.com/macosx/syncservices.html
And, periodically back up your contact, calendaring and task or to do records with, at a minimum, the facility to do so built into both the Address Book and iCal.
If such an event occurs in the future, turn off any automatic synchronization and avoid triggering any manual synchronization events until you have resolved the issue, to avoid propagating the unwanted changes across you entire synchronized device pool.