Just remove them and replace them with new shingles of a similar style to the rest of the shingles on the roof.
How to repair a small hole in a shingle roof.
A hole in a metal roof system can be caused by any number of sources the hole may be from deterioration and rust or it may be from something falling onto the roof surface such as a large branch.
The first step in the repair of any metal roofing material will involve cleaning the surface.
Lay the upper sheet of tar paper 2 inches over the lower if two sheets are needed to cover the section.
Lay roofing felt or tar paper over the missing shingles.
Then spread the sealant with a putty knife.
Next use a utility knife to trim a new shingle to match the width of the space.
If a shingle is simply cracked or torn you don t have to replace it just repair it.
Start by applying a thick bead of roofing sealant under the crack.
Smaller nail holes will be permanently fixed by this method standard roofing nails would be either 3 8 inch or 1 2 inch making a hole 3 8.
Slip a hacksaw blade under the shingle above and cut through the nails that held the old shingle in place.
If the shingles are severely damaged don t try to salvage them.
Slip the top of the paper in under the flaps of the shingles above the repair.
Loosen the adhesive underneath the tabs of the damaged shingle then pull them free and discard.
Fill small nail holes with silicone caulk or roof cement.
Clean the repair area.
Loosen and remove the damaged shingles.
Press the shingle down and apply a second bead of sealant on top of the crack.
Begin by removing the shingles down to the wood sheathing and slip a strip of adhesive ice and water barrier available where roofing repair products are sold under the soffit main roof joint.
If the hole is less than an inch i would caulk the hole.
Depending on how the roofs join you may have to cut a slot to work it in far enough.