A good general contractor should be able to handle that with no issues.

Ledger boards are difficult to flash and when the flashing is aluminum the pressure treated wood and standing water will quickly destroy it.

A skilled carpenter should be able to repair it as long as they do not use aluminum; use Grace Vycor under the metal flashing, and pull the decking and siding away from ledger so air can get to those porous materials and water flow is not obstructed. A slope to the metal flashing helps.

Structural repair of the rim joist may require more work.

A poster once recommended Maine Deck brackets to keep the ledger boards clear of the wall.

The ledger board is probably in good shape as the deck was replaced last year and no problem was noted. Why I had thought to examine behind it as well! Any thoughts on what can be done with the rim joist? Is it as simple as revealing by cutting away the ledger board, then cutting out the damaged wood and replacing it? FInally bolting on a ledgerboard and reassembling the deck?

From your description, the rim joist is rotted and must be replaced. To do this properly, the slider door has to be removed. The subfloor is attached to the rim joist, and the slider sits on the subfloor. There is probably a nail fin around the slider on all 4 sides, nailing it to the studs, header, and rim joist. When you take it out, you will be able to see the extent of the damage.

Careful deconstruction of the deck and slider door will save you money. This is a pretty big job, very labor intense. Hopefully the subfloor is still in good shape, or part of that will also have to be replaced.

When putting things back together, make sure the door opening is flashed properly. It should have sticky flashing on all sides and underneath, covering the framing, subfloor, and the rim joist, sticking to the house's weather barrier of tar paper or tyvek. Another layer of sticky flashing goes over the nailing fin. The metal flashing installs over that, tucking under the sill of the slider and over the ledger board. Another piece of metal flashing should tuck in behind the bottom of the ledger board, and come out over the siding below.

I can see from underneath that there is a thin strip of plywood subfloor placed under the slider which needs to be replaced as well. As it is a strip, it doesn't seem to be much effort to replace. But the rim joist must be replaced the entire door length. I opened the rim joist insulation so I could see the extent of the damage and it only extends beneath the door.

Aidan, is there a schematic somewhere showing the correct flashing technique for the door? I'm not confident all contractors will do it right.

Google it, there are tons of sites with just this information.

It will be a month or so before the work starts. While I expect the new door flashing to prevent this problem from reoccurring, shouldn't the rim joist replacement be made of treated lumber? Any reason not to buy PT? I will seal the wood on the inside for insulation purposes so I see no issue of chemical exposure. But if this is such a good idea, why isn't my rim joist already pt?

Treated lumber is not suitable for structural applications.

The chemical treatment process weakens the wood significantly.

The only members that should be treated wood are the sill plates. The sill plate rests on a continuous footing, thus there is no span. The rim joist should be #1 structural grade timber, Douglas Fir or Southern Yellow Pine.