Yeah it sounds like its growth has already been stunted. If you transplant it won't kill it but it will stress it even more. With autos you want to plant directly into soil don't even germinate in paper towels. So I would say leave it alone and maybe start another in like a 3-5 gal pot.
U can trasfer with no stress at all. All u do is put the smaller pot in the bigger one with the bottom cut off an a slice up one side, the riots will grow into the bigger pot then as they grow more into the big pot just slide the smaller one out, if their clay pots u gonna have to break the bottom carefully an add some white shark root trans powder to lower the stress an it should be ok.