I think that you are quite correct that he owned/carried a number of firearms.

Here's some that I have recorded:

#20233 COLT MODEL 1860 ARMY NON-FLUTED CYLINDER – Carried by General Robert E. Lee. Carried for the duration of the war.

#2 HENRY DERINGER SINGLE SHOT PISTOL – .41 cal. Marked “Deringer, Philadel’a”, “Wolfe & Durringer, Louis’e, Ky, Agents”, and “R.E. Lee”. One of pair owned by Gen. Robert E. Lee.

#3 HENRY DERINGER SINGLE SHOT PISTOL – .41 cal. Marked “Deringer, Philadel’a”, “Wolfe & Durringer, Louis’e, Ky, Agents”, and “R.E. Lee”. One of pair owned by Gen. Robert E. Lee.

The above set of Deringer's probably included a third firearm (which would have been "#1" in the set).