Yes, in retrospect I should have realized that the DocType Structure was what the constraint required rather than the calculated value in the Name property. Sorry for any head-scratching I might have caused

You shouldn't need to ...

DEV>Set msg = ##class(EnsLib.HL7.Message).%OpenId(29485840)

DEV>Write msg.Name
ADT_A11
DEV>Write msg.GetValueAt("MSH:9")
ADT^A11
DEV>Do msg.SetValueAt("A08","MSH:9.2")

DEV>Write msg.GetValueAt("MSH:9")
ADT^A08
DEV>Write msg.Name
ADT_A08

But I guess it wouldn't hurt 

Is it possible that there's an action somewhere in the DTL that clears MSH:9?

I've written a query for HL7Spy's SQL Loader that extracts ACKs/NAKs from the IOLog:

Here's the SQL in text form. The method HICG.GetMsg() is an ObjectScript stored procedure written specifically for HL7Spy that returns the message body as a stream for delivery via ODBC. You could adapt the SQL for use with the %SQL.Statement class to return a result set containing the message body IDs, Next() your way through that, open each message with %OpenId() and write it out to a file. Getting just the NAKs will require a bit of message parsing.

SELECT  
  head.ConfigName As ConfigName,
  body.DocType As DocumentType,
  body.Name As BodyName,
  HICG.GetMsg(body.ID) As Message
FROM
  Ens_Util.IOLogObj head
INNER JOIN
  EnsLib_HL7.Message body
ON
  head.InObjectId = body.%ID
WHERE  -- specify start and end time for search here
  head.ID >= (SELECT TOP 1 ID FROM Ens_Util.IOLogObj WHERE TimeReceived >='2022-06-01 00:00:00.000' ORDER BY TimeReceived ASC)
  AND head.ID <= (SELECT TOP 1 ID FROM Ens_Util.IOLogObj WHERE TimeReceived <='2022-06-02 00:00:00.000' ORDER BY TimeReceived DESC)
  AND head.IsInbound = 0
  AND head.InObjectClass = 'EnsLib.HL7.Message'
  AND head.ConfigName = 'To_Outbound_Operation' -- substitute operation name here

Assuming you cut and pasted from your DTL, the double-quote characters around the 2nd dash are incorrect. They appear to be the distinct open and close quote characters that Word automatically substitutes for the "standard" double-quote character:

set            tSSN                                                                  source.{PID:SSNNumberPatient}                               
set            target.{PID:SSNNumberPatient}                  $E(tSSN,1,3)_"-"_$E(tSSN,4,5)_”-“_$E(tSSN,6,9)

If you create the following class in IRIS Studio, a "FormatSSN()" function will be available in the DTL editor's expression editor, and you can use it in your set rules:

Class Misc.Util.StringFunction Extends Ens.Rule.FunctionSet
{ 
ClassMethod FormatSSN(pStr As %String) As %String
{
   Set tStr = $ZSTRIP(pStr,"*AWP")
   Return $E(tStr,1,3)_"-"_$E(tStr,4,5)_"-"_$E(tStr,6,9)
}
}

The method strips all non-numeric characters from the value passed to it, then formats it per the SSN format. It doesn't verify that the proper number of digits are present, but that's something that can be easily added.

In a DTL action, it would look like this:

<assign value='$PIECE($ZCVT(source.{ibex_medical_chart.patient_info.admdoc.name},"i","XML"),",",1)' property='target.{PV1:AdmittingDoctor(1).FamilyName}' action='set' />
<assign value='$PIECE($ZCVT(source.{ibex_medical_chart.patient_info.admdoc.name},"i","XML"),",",2)' property='target.{PV1:AdmittingDoctor(1).GivenName}' action='set' />

Or a bit more efficiently:

<assign value='$ZCVT(source.{ibex_medical_chart.patient_info.admdoc.name},"i","XML")' property='tFullName' action='set' />
<assign value='$PIECE(tFullName,",",1)' property='target.{PV1:AdmittingDoctor(1).FamilyName}' action='set' />
<assign value='$PIECE(tFullName,",",2)' property='target.{PV1:AdmittingDoctor(1).GivenName}' action='set' />

Note that this isn't actually replacing the comma character so much as it's splitting the full name value supplied in the source path on that character and assigning the individually extracted values to their associated HL7 components in the Admitting Doctor field.

Depends on how the attachment is stored by the sender. If it's a binary attachment, the file data will be represented as a stream object in Part.BinaryData. If it's text data, Part.TextData. You just need to create a %Stream object and copy Part.BinaryData (or Part.TextData) to it:

Set stream=##class(%Stream.FileBinary).%New()
Set sc=stream.LinkToFile("/path/to/"_Part.FileName)
Do stream.CopyFrom(Part.BinaryData)
Do stream.Flush() // may not be necessary
Do stream.%Save() // ditto, but better safe than sorry ya know?

You can determine the type of data in the Part via the IsBinary boolean property ... 

You would only need to remove the repetition value from the argument passed to GetFieldNameFromNumber(); you would still continue to pass the full field index to GetValueAt(). Something like this:

set segment = msg.getSegmentByIndex(3)
Set fieldIndex = "3(2).1"
Set fieldNameIndex = ##class(User.Util.StringFunctions).ChangePattern(fieldIndex,"(\d)","()")
set fieldName = ##class(EnsLib.HL7.Schema).GetFieldNameFromNumber("2.5", segment.Name, fieldNameIndex)
set fieldValue = segment.GetValueAt(fieldIndex)

The ChangePattern method:

Class User.Util.StringFunctions Extends Ens.Util.FunctionSet
{
ClassMethod ChangePattern(pStr As %String, pPat As %String, pRep As %String) As %String
{
	Set tOut = pStr
	Do {
		Set tLoc = $LOCATE(tOut,pPat,,,tFnd)
		Set:$DATA(tFnd) tOut = $REPLACE(tOut,tFnd,pRep)
	} While tLoc '= 0
	Return tOut
}
}