This is a tuffy. Wood Flooring is laid down sometimes WITH, and sometimes WITHOUT an adhesive under it. Common denominator is brads are shot through it to hold it down... Putty is then used to mask where the nails (brads) are.
If the brads don't go as deep as they should, traffic on the floor can catch them and bring the heads up.
About the only options are to use a center punch to drive the heads of the nails below the floor slightly, and then putty them a matching color. Or pull them up, re-nail in a new spot, and mask accordingly.
Or as a last ditch effort - (short of a new floor) put a dab of liquid nails in the hole a brad came out of, and drive a finishing nail in to the correct depth and putty the dimple.
STAPLES can be used, but they should be shot so that they go with the grain of the wood pattern.
If nothing works, there is a question as to the condition of the wood that the flooring is being attached to. THAT can get ugly...
It can lead right back to a leak situation, and that would imply other damage.
I will say this also -
Anywhere you replace rotted wood, either treat it or paint it.
Untreated wood (normally press-board) is common in older trailers. Paint or wood treatment can stave off a lot of future headaches.
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