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I want to install a pergola over a space out my back door. My plan was to cap and remove the gutter from a section of the fascia and attach a ledger board (secured to the rafter tails).
What I'm not sure about is the aluminum trim currently covering the fascia. Should I leave this in place and sandwich it between the fascia and the ledger or remove it and replace it with some other covering?
You should probably leave all weatherproofing in place. The key is to prevent water from draining into unwanted areas, which means that you may want to add flashing to move the drip edge outward and over the ledger. Whether and how you'd do that depends on your pergola design.
You may also opt to simply seal all penetrations through the fascia cover by sandwiching a rubber or foam layer. Moisture will have a tendency to soak into that joint and through nail or screw holes.
