In an Active-HDL workspace, there is a known error when the source files are organized into folders. For instance in the Design Browser tab, a user may create several folders. The source files can then be dragged and dropped into these folders for organization. Once this is done, links to the source files in different design files won’t be updated until the workspace has been reloaded.
To resolve this, simply reload the project. This can be done be executing the following from the console: workspace open <PATH_TO_WORKSPACE>