I was replacing a sliding glass door and came across a nice discovery
on my 1968 house in CT, lots of rotten wood and water damage. The deck
is attached to the house with a ledger, but I don't believe there is
any flashing. THe bottom few inches of the sheathing under the
aluminum siding is completely rotten and just falls apart. I obviously
should remove the aluminum siding and add some sort of flashing, but I
am not sure I can safely remove the ledger board to get behind it to
install the flashing. Any ideas? Can I install the flashing over the
ledger?
Thanks
Jeremy

This will sound cantankerous, and I should preface this by saying I
hate decks both aesthetically and for this sort of reason.

But anyway, if it's that big a mess you'll need to dig in and see if
you have termites, carpenter ants, mold, or more extensive damage.

(I am off now to spread more cheer !)

Your situation is - unfortunately - common.
Look for:
pan flashing below the door threshold.
flashing over the ledger.
It sounds like this doesn't exist.
Rain splashes up from the deck and blows along the deck, putting a lot
of water at the line where the deck meets the main building. It takes
special care that's seldom given to manage the water.
I don't know of any books or web sites that address the problem.
Your best bet is a well respected contractor or an architect.
TB