The MapReference property is not saved when you call the Channel.Save method, and the Reference property is not saved when you call the Document.Save method in BizTalk Server

Set BT = CreateObject("BizTalk.BizTalkConfig")
Set chan = BT.createchannel
Set rschan = BT.Channels

While Not rschan.EOF
      chan.Load (rschan("id"))
      'Save a copy of the MapReference property.
      szMapPath = chan.MapReference      
      chan.MapReference = szMapPath
      chan.Save
      rschan.MoveNext
Wend

Set chan = Nothing
Set rschan = Nothing
Set BT = Nothing

Set BT = CreateObject("BizTalk.BizTalkConfig")
Set doc = bt.createdocument
Set rsdocs = bt.documents

While Not rsdocs.EOF
    doc.Load (rsdocs("id"))
    'Save a copy of the Reference property.
    strRef = doc.Reference
    doc.Reference = strRef
    doc.Save
    rsdocs.MoveNext
Wend

Set doc = Nothing
Set rsdocs = Nothing
Set BT = Nothing