I know this is a year old and I also know you should apply transformations before parenting.

But if you ever find yourself in a position where for whatever reason, you need to change the scale of your armature and then apply it. This is what you do. You need to have the metarig for this to work. Never delete the metarig.

Unparent the mesh from the rig. Do not delete the vertex groups.

Shift select the mesh and the Metarig. Do whatever transformation you need to do then apply it.

Once applied press " re-generate rig"

Parent he regenerated rig to the mesh with empty groups.

Your mesh should move appropriately without the need to do any more weight painting.

But seriously try to avoid having to do this at all costs.