I ended up resolving this by manually editing the scene files and removing references to PackedScenes in certain scripts. I had seen mention of 4.x having issues with cyclically referenced scenes, so that's likely the issue.

Were you hoping for the acquisition to be denied? I'm curious to hear if/why people think this going through will be bad.

It shouldn't be too difficult to redo, especially if I use the original tscn content for reference. It's the main menu UI and the only error I saw was related to textures I'm using for the buttons. I have a sneaking suspicion that it could be the TextureAtlas I created for the UI. I hadn't thought of launching from command line, that's a good idea!

For further context, I am using git and the only change that happens after the upgrade is a string changed from 4.0->4.1 in the project file.