Large water changes in a neglected tank can cause problems. This is not an issue of changing too much water too often, but of not changing enough water often enough. The water parameters in the tank are usually vastly different from tap water used to replace it.
Buildup of waste products often drops the pH, usually increases hardness, as people tend to just top off a neglected tank to compensate for evaporation, and always results in an increase of total dissolved solids. When a large water change is done on a neglected tank these drastic changes can be at the very least stressful, and at worst deadly for fish.
Ammonia is less toxic at lower pH levels, when the pH is increased in a situation like this the ammonia, which is actually much less toxic ammonium at lower pH levels, converts to ammonia. The sudden change in hardness & TDS causes osmotic stress on the fish, the combination of the two can be really rough.
In a situation like this, often referred to as "old tank syndrome", it is best to do some small 10% water changes every other day for at least a week, two is better. This lets the fish slowly acclimate to the new water parameters, with less stress from the changing levels.
