Hi @James777, no sure what happened, but in the 3.5 folder, your custom qualities are indeed missing. I tried removing the 3.5 folder and then start Cura 3.5, which will upgrade using your existing 3.4 folder, and that worked for me. Could you try that, too?
Remove the following folders:
C:\Users\<your-user-name>\AppData\Roaming\cura\3.5
C:\Users\<your-user-name>\AppData\Local\cura\3.5
Start Cura 3.5