[jigsawlogic]

This is really a question about vision vs. execution. Hopefully, we're talking about a situation in which the former is present, but the latter is questionable.

Recording is more or less a virtual art--for better or for worse--meaning that it is possible to project a perfected version of one's aims, regardless of instrumental technique. But there is still a separation between actual and virtual. By replacing a performer's recorded performance with your own, you blind him to the reasons for doing so in the first place, and he will perceive the virtual as actual. You, as the engineer, have thrown your good coat down over a puddle to allow poor musicianship to walk across without getting its boots wet. And that allows poor musicians to continue in the illusion that rain only wets "the other people", rather than perceiving their faults and mustering up the gumption to correct them.

When engineers, as a collective, complain about the fact that poor musicianship interferes with their craft, they only have the more virtual aspects of their craft to blame. The engineer's toolbox must share the same lid as Pandora's...once open, people who can't play or sing have a level playing field with those who have shed blood and sweat developing their natural talents. In the days of real time recording, the people you complain about wouldn't even get past the door, and questions such as this shouldn't exist. You do a disservice to both the artist, and the rest of us, by replacing his parts on the sly. The artist, by removing any evidence of his lack of skill, thereby insuring that he will never improve. The rest of us, by insuring that someone like him will walk through the door.

At the very least, play his own bass part back-to-back with your replacement. Point out to him what you did, and why you did it. If, on the other hand, you decide that discretion is the better part of valor, then know that when you read another post about a terrible band that can't play, you have helped contribute to the problem.