I repair these roofs, although somewhat infrequently. I gave up on
replacement of the nails with screws as getting the nails out turned
into a real problem.

Dented tin, wallowed out holes, and snapped off nail heads. I made
more work than I started out with.

Go buy some Sonneborn NP1. It is an elastomeric UV resistant caulk,
and it is all I use for my roof repairs, and has been the only thing
for the last 10+ years or so.

Put your sheet of plywood up on the roof so you don't misstep, crinkle
or dent your deck. (The sheetmetal is only 29 gauge, and a probably a
low quality at that.) Take you caulk gun, a roll of paper towels, and
a stiff brush on the roof.

Brush off the nail heads to clean them. The gasket may come off, but
that isn't important. Make sure the nail is secured and hasn't backed
out (drive it back in if you have to.) Put a wad of NP1 directly on
the nail head and rub it in a circular motion around the nail head,
and then lift your finger off from the center. You should have
something that looks like a Hershey's kiss. Next screw.

Spec writers for commercial roofing plans call this encapsulation, and
it works. Whenever we do sheetmetal repairs on chimneys, flashings,
caps, anything that has screws or rivets in it we always use this
method.

The only screws I would put in would be if the roof was loose, it
rattled, or the nails let go.

Here's another tip. Cut your plywood in half so you can sit and work
on one, then move to the other and work your way around, rather than
to have to step onto the thin metal (dent!) and move a 4X8 sheet.

Robert