I am sorry for my late reply. I've just tried a couple of scenarios and it seems that we have an issue - we add a link to ~/Content/Site.css in the _Layout.cshtml no matter if that file exists or not. You can remove that link and give it another try.
Please, let us know if that is the case on you side. You can also send us the backup folder which is generated during the upgrade to take a look of you project configuration. You can find that folder next to your solution file.
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