Roofing contractors have told me electro galvanized nails that stick out past the sheathing edge can attract water which can prevent the wood deck from absorbing the moisture and rotting.
Roofing nails protruding.
Use the grip rite 11 x 1 1 4 in.
3 degree electro galvanized steel roofing nails 5 lb pack for applying roofing asphalt shingles insulation board and felt to wood substrates.
A large nail head and heavier shank gauge provide greater holding power.
The protruding nails will help hold it in place there are also adhesives for foam that come in std.
Hammer a new nail into the roof about 1 inch above the hole from the previous nail.
Our contractor said b c our decking was so thin 3 8 the 1 1 4 nails protruded but its ok b c if he used 3 4 shorter nails it would risk.
3 use the grip rite 11 x 1 1 4 in.
Roofing nail should have a barbed shank until the head which eliminates nail pops blow offs and roof leaks.
Or there is spray foam insulation to consider if that works with your other insulation and vapor barrier situation.
Protruding nails can actually be a good thing.
For example galvanized by various processes aluminium copper or stainless steel.
A roofing nail should have a minimum nominal shank diameter of 12 gauge 2 67 mm and a minimum head diameter of 9 5 mm.
Of the cutting methods the cut off wheel sounds the best to me.
Most protruding 3 or so into the crawlspace.
If you have a friend in the attic ask him to direct you to a sturdy spot where the nail can bite into the wood.