At the same time, it's BizTalk that is crashing here and that requires BizTalk to fix that issue with itself. It shouldn't be doing that regardless of anything WinSCP does.

Thanks. Can you please find out for us what is really the latest version that still works? It may help us identifying what change broke the compatibility. And possibly make the up-to-date version of WinSCP compatible again.

Alrite after some more time put into this I back all the way back to WinSCP 6.1.2 (Says 6.1.2 or later on Microsofts CU5 update for BizTalk). This version seems to be working (while later versions does not).
Havent tried each version ofc. But there is something missing in the newer versions that BizTalk uses it seems.

Is this really all you got?
Because the actual exception message is missing.
The message should be like "Method not found: METHODNAME".
Without that information, it's hard to tell, what the problem is and if it is even WinSCP related.

Same problem (I see you have posted there already):
Hotfix for Biztalk Server SFTP Adaptor - Microsoft Q&A

After searching the web for a while I've seen a few posts with my exact problem and no responses at all.
After installing the latest Cumulative Update (CU5) for BizTalk 2020 we have gotten the following error for our SFTP-adapter.

Application: BTSNTSvc64.exe
Framework Version: v4.0.30319
Description: The process was terminated due to an unhandled exception.
Exception Info: System.MissingMethodException
at Microsoft.BizTalk.Adapter.Sftp.SftpFileReceiver.PollSftpServer()
at System.Threading.ExecutionContext.RunInternal(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object, Boolean)
at System.Threading.ExecutionContext.Run(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object, Boolean)
at System.Threading.ExecutionContext.Run(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object)
at System.Threading.ThreadHelper.ThreadStart()"

After some searching on the web several other people have the same problem and it seems to be some sort of WinSCP mismatch.

I have tried version 6.3.3 – 6.3.5 with no luck. Also tried WinSCP-6.3.5-Automation.zip-pack and all the different versions of WinSCP there (netstandard2.0 and net4.0) (I swapped both the DLL in the install directly and the one that is put side by side of the Microsoft.BizTalk.Adapter.Sftp.dll in the GAC.
Except for the few hits on other people with the same error I really don't know where to turn. Don't know if the error helps in any way but its all I'm getting from the Windows Logs