What problem are we chasing now? The “Object reference not set to an instance of an object” is so generic an error message that it means little in Duplicati terms without a solid understanding of the code area, and a reproducible test to look at. I lack the former (any readers know Duplicati/Server/WebServer/RESTMethods/CommandLine.cs and its WriteLine?). I set up a debugger, but was not even using that code on my backup.
If that problem has somehow vanished, the “Unexpected difference in fileset”, though of unclear origin, has a simple workaround to try, of deleting the troubled fileset (version of the backup) shown in the error message. Here is a recent report of success, however if the original “Object reference” still happens, I can’t help further without additional assistance from the community, or you being able to discover a way that I can reproduce it. Seeing a simple test succeed is encouraging, but the key is figuring out the difference between it and failure.
For additional information on how to use the delete command for the “Unexpected difference” error, see this, and please feel free to clarify the relationship between these two problems and which is the current problem.