I had some staples same way. I made a small cut and they did not appear to be attached to any wood underneath. I pulled them, ran a screw down level and covered it with a Eternabond patch.
Mine was way out of warranty before I noticed it enough to address it. They never came thru the roof membrane.
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2011- 351RLTS Eagle, MorRyde suspension/pin box,
2017- F350 6.7 PSD Lariat FX4,SRW, SB,CC
Hughes PWD SP-50A, TST TPMS
Gator roll-up bed cover
B&W Turnover ball, Andersen Ultimate 3220
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