How do I fix crystallized butter cream filling made with ghee?
One problem is, making a larger batch just may not work - especially since this recipe needs a lot of precision in timing.  Specifically, the need for it to be mixed while hot makes larger batches problematical.  The second point is, the recipe states it can't be made in advance - which makes maintaining it at temperature, or reheating if it cools too much during filling, very problematic.  For the future, I would recommend making each smaller batch sequentially.

Is there anything you can do to fix it?  Maybe not exactly as intended, but I think adding a bit, a little bit, of water may work - it should loosen the filling enough to reach creamy consistency.  At worst, this batch of cookies may have a softer filling - which is not a terrible fate, even if not ideal.  But if you use very less water, and heat the filling when re-mixing, especially with smaller batches, you may lose enough water to evaporation (in the heating and cooling) to minimize this effect.

I would suggest making a few very small test batches to see how the filling holds up to these ideas - how much water to add, if heating (post-water addition) helps the texture, if the taste is still good, even if the filling as-is would be okay once in the sandwich.