I created a little application to show this problem. The application can be found at https://www.dropbox.com/sh/ku5526j90pbds5p/BnfWCQ6wwF. The required jar (jimStlMeshImporterJFX.jar) and STL is also in the directory. Copy the stl file locally and change FILE_NAME to point to the new file location. Java should be able to read and write to the location.

This is what the application does
Loads an STL file into a TriangleMesh
Store the original data points into an array
Moves the object using setTranslateX, setTranslateY and setTranslateZ
Compare data points after move to original data points
Saves the object to an STL using the same name. The new file is in ASCII so that it is easier to see changes.

The internal data of the TriangleMesh doesn't update using the translate methods and there doesn't seem to be a way to force updating the data