Certain normal vectors of facets get flipped when I load a saved molflow 2.6.71 file into the 2.6.72 version.
Yes, in fact one of the fixes in Molflow 2.6.72 is enforcing the right-hand rule rule (the indices increase according to your right hand if your thumb is pointing towards the normal).
In previous versions, the first turn decided the normal vector direction, which means it wasn't well-defined in case of concave facets. You can test it: in previous versions: if you issue the Facet / Shift Vertex command on a concave facet, the normal flips randomly based on where the first index is.
A drawback is that indeed, concave facets saved with previous versions might either flip normal or not, depending whether they obeyed the right-hand rule so far. Please fix these manually, and once saved with the new version, they are guaranteed to behave well in the future.