Hi Joe @Merijeek,
This comes with a warning; this is especially true when working with Meshes:
Please do not get into the habit to Apply All Transforms (‘ever’). Only Apply the Scale (‘always’).
You might sometimes want to ‘reset’ the Rotation and/or Location with ALT+R and ALT+G, but Applying the Rotation should be avoided (if possible) and Applying the Location is almost never what you want. Applying a Transform is done to the Origin (Coordinate System) of an Object, leaving the Mesh as it is (visually), while Clearing a Transform sets the whole Mesh (with its Origin) back.
Now, an Empty is just an Origin, so Clearing and Applying a Transform does exactly the same thing (i.e. has the same result).
