WinSCP changes the window as needed during the session.

You cannot disable this, but you can limit the window size somewhat by disabling Optimize connection buffer size:
https://winscp.net/eng/docs/ui_login_connection

What is causing winSCP to adjust the window size as the transfer occurs and is it possible by an option setting to disable the behavior?

That's correct.
Unfortunately the message does not say, what the size was and why the server considers it "bad".

Maybe the server has some limit on the window size that WinSCP exceeds. But that's just a guess.

Yes, message is generated at the server side (Tectia zOS) and as far as I can tell from what I can find on the subject it is in response to a directive from the client.

"Bad window size in WINDOW_ADJUST": Is that an error you get on the server or what?

WinSCP Version 5.5.1 (Build 3970) (OS 6.1.7601 Service Pack 1 - Windows 7 Enterprise) client of SSH Tectia Server 6.4.7 on i370-ibm-openedition running on zOS 2.1. User tries to download approx. 1.2GB file, appears to be doing text conversion to ascii, after approximately 30 minutes it fails. Log available if that might be useful. What should I have the user check in their session setup?

Askng the same question of Tectia vendor to see if they have any insight.