When you open the project in PSoC Creator, do you have to update any components to build?
If so, have you read the Component Changes section to see if there are any component changes that might affect the functionality of your project?
If you double click the project / workspace, it will open in the last installed PSoC Creator version by default. It seems that your project is opened in PSoC Creator 4.2 atleast once. If you have project backup, please continue to use Creator 3.3. Else, please use Creator 4.2 instead of Creator 3.3.
Thanks, you were right.
After I restored the project from a backup that has never been touched by PSoC Creator 4.2, it worked again.