You could try freezing your scale and rotation before applying the xform (alt + right click > freeze scale/rotation). You probably already know this, but you should never scale a mesh at the object level.
This can also happen if the object is part of a hierarchy.
The transform of a parent will affect the transform of its children, so if you use the Reset Transform utility on a parent object, the children might change drastically.
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You probably already know this, but you should never scale a mesh at the object level.