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can I reinstall the remilled planks by nailing only?
Only if you are face nailing.
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Even if I install the proper waterproofing and sub floor
You need to isolate the source of the moisture and fix it at the source. If for some reason you are still experiencing too much moisture you need to use a product like MVP. If the sub floor is already laid you can install it over the sub-floor but ideally it would be applied to the concrete.
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Wonder if moisture can migrate up through the nails in the concrete from the sub floor
No metal does not allow water vapor transmission, what can allow for it is the void the nail creates in the sub-floor. Go over each nail with some asphalt caulk to seal the hole.
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Someone at NWFA recommended gluing the sub floor to the concrete, but that seems risky...what if the plywood pops from pressure? What if the urethane doesn't hold due to expansion or general shifting of the plywood?
Under normal conditions this should not be a concern, if it is then you need to look into a floating sub-floor.
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What if I use two layers of felt above the subfloor after applying the concrete adhesive, overlapping the edges 12", staggering the two layers, then nailing the walnut planks to the subfloor, no glue.
Don’t overlap the seams you will cause ridges in your floor. Two layers will make it mushy.
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Can I use 5/8" plywood, or does it have to be a minimum of 3/4" over concrete?
If you are installing ¾ solid you need ¾ plywood. You can install on 5/8 at a minimum by ¾ is recommended. If you do the floating system it is two layers of ½.
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Also, can someone tell me if tung oil or another non-urethane product can be applied to the surface which can be reapplied without sanding the surface again? I don't think I could survive the sanding and restaining process again!
If it has not been finished tung-oil can be reapplied.