What type of exterior siding does your house have? Did you see any holes in the exterior wall when you opened up the interior for the new patio door?
It is very likely that the original installer loosened up, or removed, a run of siding, drilled a hole through the exterior wall sheathing, then reapplied the siding. If it can be determined what was originally done it may reduce the headache.
hth, Doug
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