With out the long explanation from above how did you do it?
Our practice was to create the blank database in SDE with Web Mercator as the projection for each dataset.
Or original data was in UTM Zone 15 and it caused issues near the ends as it extended into zones 14 and 16 and was seriously warped.
When we did it we simply selected all the feature classes in the UTM dataset, and pasted them into the Web Mercator dataset. And our world was straightened out.