If you no longer want a Truffle project linked to a workspace, go to the
WORKSPACE settings pane the same way you did when linking the project.
To remove/unlink a Truffle project from the workspace, click on the project file in the
TRUFFLE PROJECTS list and then click the
REMOVE PROJECT button.
When you're done, click the
SAVE AND RESTART (
SAVE WORKSPACE if this is a new workspace) button in the top right.