I can not answer for JR, but I have seen over the years, quite a few Engines removed from the Freeware Downloads area, never to return, simply due to their age, and compatibility with newer Trainz versions.
I have also seen, and experienced, buying a payware item, only to have it moved to the Freeware area just a few weeks/months later, for the same reason .. they are simply older products, and room being made for new stuff.