Well, according to Tsunade, the damage cuts off the chakra circulatory system. If the chakra path to the cells itself is cut off, no amount of supercharged Kyuubi powers will heal them.

As for the damage being reversible, not all bodily processes are. For example, chronic binge drinkers can develop hepatocirrhosis (scarring of the liver), which is where damaged/destroyed cells are replaced with connective tissue incapable of liver function, decreasing overall liver function each time despite it having "healed".

The same can be thought of about these chakra circuits. Either that, or perhaps it's like brain cells or enamel - your body simply can't replace it.

As for Sasuke having trouble sustaining his chidori, who knows how long he's been training for. Last time we heard, he's only capable of using it twice.