Wi: Robert E. Lee had a different Career

Recently I got a book from my local library on the Southern General. In it, the author wrote that Lee had some success as a civil engineer. My question is, what if Lee had remained a Civil Engineer?

Who would take over Harpers Ferry raid and who would lead the Confederate forces?

Plus the most obvious question, How would this alternate Civil War end?
 
Perhaps Stonewall Jackson could take Lee's place. CSA is still going lost the war. It was quiet unwinnable for them. But it might end bit faster.
 
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