Well, I did not have that exactly right. Your post made me go back and look at my CD, and then go to the web for clarification.
Check this link: http://www.lukpac.org/~handmade/patio/vinylvscds/money.html
What happened is that Zappa originally remixed and reissued "We're Only In It For The Money" on a CD which also contained "Lumpy Gravy", in 1986. On this 1986 CD, he erased Roy Estrada's bass parts and Jimmy Carl Black's drum parts from "Money" and had Arthur Barrow and Chad Wackerman record new parts. It was Wackerman, not Terry Bozzio. He claimed at the time that the original tapes were in such poor condition that he had to do that.
I have a copy of the 1986 CD reissue. To me, "We're Only In It For The Money" does not sound right with the different bass and drum parts, as I am very familiar with the vinyl version (actually, versions, considering how many partially censored vinyl versions were released). It may be that Barrow and Wackerman were more technically skilled than Estrada and Black, but to my ears, there is a definite loss of feeling, of soul if you will. Also, there are odd little moments where Barrow or Wackerman really stick out where I think, oh no! It sounds to me like it would if someone dubbed Eddie Gomez over the original Jimmy Blanton bass parts on the 1940 Ellington classics.
In 1995, a new CD reissue of "We're Only In It For The Money" was released, with the original bass and drums parts by Roy Estrada and Jimmy Carl Black present. There is no audible damage to their parts, so the "poor condition of the tapes" idea seems to be incorrect. I like the 1995 CD reissue much better.