I apologize. This worked exactly as I wrote it when I did these steps this morning. However, I have the same issue as Jumping Mammoth when I checked the file this afternoon. Gah!
No matter. I have a solution.
Edit: Never Mind. I’ve found yet another bug*
In the original file that you linked, (make sure it has not been tampered with) select the armature in Pose mode, Scale the Root bone (only) to make the character whatever size you where after.
Next Enter Object mode. With the armature selected, CTRL A, Apply Scale.
Next select the mesh (character body) in Object mode. Alt-P, Clear Parent Keep Transform. Next CTRL-A, Apply Scale. Then, with the mesh still selected, shift select the armature, CTRL P, Armature Deform.
That should do it.
I did this three times on my machine to make sure the steps where correct. Worked all three times for me.
End Edit:This will not work
None of this is really necessary as that is what the root bone is for, scaling the whole rig to the size you need the character in your scene.
P.S. Skip, you where on to something with the stretch to’s. Unfortunately the IK’s were also breaking. It must have something to do with the Rigify Code. I’ve never encountered this on a home made rig.
P.S.S With yet more testing…Resetting the Stretch To constraints worked after applying the scale. The IK “bug” seams to be only visual. (Big black lines skipping all over the place.) Still…Not sure why the OP needs to scale the armature and apply that scale when that is the job of the root bone.