Although they may have not bin cedar chips, I have used this method once,
and will never again. This caused an even worse infestation of gnats and added mold to the situation, it may have bin my chips but who knows..
But considering he didnt ask for a gnat solution i feel this is irrelevant since he is already using neems and sand which in my opinion is a much more sterile and healthy solution that has worked well with me countless times.
as for your roots
I have never had to REPAIR my roots after gnats, generally they are just happy the gnat larvae are gone, but i like natural solutions to root health, First of all the best stress reducer and root helper is seaweed so any seweed ammendment to ur water is good, I use MaxiCrop, its cheap and good. Second I make sure the benifical bacteria and soil life is florishing and happy, this involves adding the little warriors with any product like Sub Culure, Mayan madness, Or Tranchala and pirana from advanced (waist of money), The second part to this is feeding them, this is done by adding black strap molasses, and they will convert this into calcium and other natural micro nuitrient.