We have changed the way updates are done towards MS Dynamics NAV. If Table Link specified is not unique, then we will loop through all records in destination and update all these records (if the values are different from the source field list). It can be disabled using the parameter NavisionDoUpdateMultipleRecords in the rapidi.cfg file.
Do not use "Disable Dest Lookup" in connection with this feature, just use a normal Update Transfer. It will do statistics correct and count all updated records in NAV.