smart object issue and questions

When you edit the object it will not be rotated. The Smart Object layer is what is  rotated. When you open the layer smart Object you edit the object you are not  editing the Smart Object layer.  The smart object Layer Object transform may scale rotated and distort the object for the layer use of the object and its will not change when you edit the smart object.  You should not rotate, or change the smart object aspect ratio and size.  For if you do the Smart Object layer's transform will not be appropriate for the changed object. Its for the Smart object original size.  Did you add your logo as a new top layer in the Smart Object work file?   If the Smart Object was a Placed Jpeg you also need to flatten for save to work. Once the work document is saved Photoshop should update the smart object layer Object withe your changes and your logo should be visible in it. 

Check to see if the logo is not sitting off the page. Use the selection tool an select way outside the page area.