Never mind, I'm an idiot. One of my colleagues found the issue - I thought I had, but I hadn't managed to add both:

• Property ReplyCodeActions As %String(MAXLEN = 1000);
• Parameter SETTINGS = "ReplyCodeActions:Additional,...."

I think I'd added one to TNHS.SOAPclassExtra, hadn't worked, tried the other, but somehow failed to check both together...🙄 Working now.

Follow-up/solution: we can do:

set message2 = message.%ConstructClone(1)

and then use message for the XML generation and message2 for calls to GetValueAt, and that works OK.

Still don't know why GetValueAt appears to change the content of the message...

For the sake of having an "accepted" answer on this post: we never got to the bottom of what was going on, and scrubbed and reinstalled Ensemble. Thanks for suggestions - some useful learning, even if we were never able to get to the bottom of what was going on.

For completeness / in case others come across this, turned out the XML export file was being corrupted during transfer between the two systems. It was a CR/LF corruption - in our specific case CR/LF was getting converted to CR/CR/LF !!

Highlighted that DTL's specifically appear sensitive to CR/LF changes - we've subsequently come across the same #6301 error loading DTL's get CR/LF modified in another way (we're still tracking that one down, though suspicion currently is with git...)