Check that the intended workbook is activated, so your save action is only performed on that workbook:
Public Sub OnTimeCallback()
If ActiveWorkbook.Name = "MyWorkbook.xlsm" Then
Debug.Print "Save some stuff"
End If
alertTime = Now + TimeValue("00:0:02")
Application.OnTime alertTime, "OnTimeCallback"
End Sub
A better solution would be to deactivate the timer as long as another workbook is active, using the Workbook_Activate/Workbook_Deactivate events.