Have you checked the main.scss and are all related files correctly referenced?
Maybe the \theme\styles\web\sass folder got overwritten with the upgrade (shouldn’t happen imo).
Does the file in your deployment directory get changed at all. Check in your browser if the main.css contains any of your changes. Also check if Calypso does anything at all and if she changes the same file that you see being used in your browser.
Does this problem occur in both web and native?
Seen this before, I stopped Calypso, closed my editor, hit the Clean Deployment Directory option in the modelers Project tab, re-built the project and started up Calypso. Also try if re-selecting your projects folder and project in Calypso does the trick