Could airships (self-mobile, not simply balloons) have helped Lee with visibility before the battles of Antietam, Gettysburg, and Grant crossing the James? That's about the only way I think such (far-fetched) vehicles could have changed anything (I admit I may be inflating their potential contribution a bit...)
If he had them thanks to Basically Magic, then yes.
Practically, no.
The basic problem is that the process of doing the scouting is:
Generate sufficient lifting gas for the airship.
Load the airship with everything it needs to conduct a powered flight, including the fuel and engine required to fly upwind (at least some of the journey will be upwind) at a speed sufficient to do the scouting run.
Altitude helps, but the higher you want the airship to be (for a greater vision area) the harder it actually is to generate enough lift gas and the easier it is to miss something - don't forget that according to modern plot analysis one Japanese scout aircraft at Midway flew directly over the American fleet without seeing them!
Now, as it happens, we know the date of the first airship to conduct a powered round trip flight - take off from a location, return to the same location.
That airship was French and was launched in 1884, and it conducted seven flights (five of them round-trip flights); the first flight was a total distance travelled of five miles. This is Not Very Useful.
Functionally to do useful air recon you're probably looking at 1890s tech.
Now, if we assume an airship more than two decades ahead, here's how that could be useful in the battles in question.
Antietam - it's unlikely it would be operating east of the Cacotins, so it would first "raise the alarm" that McClellan was in the area after McClellan crossed the Cacotins. However, McClellan's column was visible from South Mountain anyway; I'm not sure there's a way you can split McLaws' wing between preventing an escape by the Harpers Ferry garrision and holding the southern South Mountain gaps.
Gettysburg - this would perhaps allow Lee to coordinate his marches better and
plan for his armies to meet at Gettysburg, but good cav recon would do that anyway.
Grant's crossing of the James - I'm not sure sufficient force could be got south in time to oppose Grant's crossing. Grant's army was
much bigger than Lee's, and if Lee stripped his lines in the north too much it would endanger Richmond.
If it was possible, though, it might compel the Administration to withdraw Grant's army (which wouldn't be the first time the Union army had been ordered north from that area.)
Interestingly though perhaps the greatest value would be noticing that Washington was almost undefended...