The conversion was to make it even more of one. They were going to take out the well deck used by the landing craft, and expand the hanger deck (and modifying the flight deck) to accomodate F-35s that are replacing the Harriers.
I hadn’t heard that they were removing the well-deck. Not sure that’s even do-able as they could simply build another USS America version of the basic aviation-optimized LHA. But it appears that the Navy has had enough of those. Now what I had heard is that they were modifying the underside of the flight deck to add 2 landing spots for the F-35.
They aren't removing the Well Decks when they modify LHD's for F-35s. The first two America Class LHA's have no well deck, but they have added them back for the rest of the class starting with USS Bougainville (LHA 8). The Navy determined the medical space, well deck and vehicle storage were more important than a few extra aircraft. Basically, the extra aircraft space completely compromised the amphib mission, and deleted 2/3 of the hospital space. The America and Tripoli are "ampib in name only", though they can ferry Marines and gear by MV-22 and MH-60, and provide great air support.