Just try leaving it until it sorts itself out.
It might help if on the launcher screen you go to the Developer Tab and check the "Show database process windows", this will add one or two icons to the bottom of the desktop which if you click on them will show what is going on in the background. You cannot close them only minimise them, they will close after you have shut down Content Manager or Trainz. They take a while to close after you leave Trainz so if they are still showing do not shut down your computer until they are gone.