Has anyone had luck upgrading a project from 4.0 to 4.1?

I have a simple GUI app I made in 4.0.3 and I have tried upgrading it to 4.1 but there always seems to be a scene that it says is corrupted. I have tried the upgrade a couple times and there's always one scene that doesn't work but the others will sometimes work and sometimes not.

Fixes I've tried:

• Deleting .godot directory before upgrading/re-importing
• Manually removing references to external resources that caused errors (textures) in the scene file
• Re-importing textures

Any other ideas would be appreciated. It's not detrimental but I'd really like to make use of the exported Arrays of custom types.