I remember one show on *** ****'s previous series where they ran a tubular stainless liner down the flues. This would probably be a more permanent solution but expensive. I had a similar problem at the top of the chimney where the corrosive gases were condensing and actually ate thru the mortar and concrete and causing spalling on the face brick. I got some pre-mixed furnace cement from the hardware store and just patched the holes from the inside of the flue liner--no problem reaching them since the corrosion was all at the top of the chimney. This may not be the perfect solution but it will be 10 years or so before I can tell you for sure how this works. Good luck.