Cannot remove fact from data model after its POJO was deleted manually

Description of problem:
Adding new object generates a POJO. If you open and delete the file and go back to Data modeler, the object type is still there. So I remove it and try to save the model. That fails with org.kie.commons.java.nio.file.NoSuchFileException presented in a error popup message.

Version-Release number of selected component (if applicable):
CR1 (community)

Actual results:
Deleting a POJO file doesn't update data model and the object type cannot be removed.

Expected results:
After deleting a POJO file the object type shouldn't be listed in data model. If it is, it should be possible to remove it and save the model.