arieschiang,
Sorry, there is no way to restore breakpoints after deleting them. But if the breakpoints are deleted from the “Breakpoints view”, Ctrl-Z will undo them. Once MyEclipse is closed, though, undo isn’t possible. So, when you delete the breakpoints from Breakpoints view clicking CTRL+Z (undo) will restore the breakpoints until MyEclipse is restarted.
Form the next time onwards, I suggest you save your breakpoints regularly using File -> Export -> Run/Debug -> Breakpoints.
Let us know if you see any issues.