The kind of electronic matching analysis they were doing looks like a very sophisticated version of a Google search one of us might do on some topic or a police department running a computerized check on a set of unknown fingerprints found at a crime scene. In any such situation a lot of irrelevant information is going to be turned up along with valuable information. Then it's up to the humans to take over from the computers and do some serious analysis.
Any search of publicly available materials regarding relations between the U.S. and China is going to turn up large numbers of high ranking people in the foreign policy establishment who have extensive, legitimate relations with the Chinese. Then the analysts need to dig deeper to find out who has the illegitimate relations. It looks to me like Condi and others were turned up in the first, broad computer run and this was used as a pretext for shutting the operation down because those who shut it down were concerned about the illicit contacts between the Clinton administration and the Chinese that were probably in the pile. That's much like getting a pile of possible fingerprints from a computer search and shutting down the final analysis to protect the real perp.
In early 2000, GWB hadn't even been elected yet. Condi wasn't even at the State department (in any capacity) until almost a year later. AFAIK, she had no position with the clinton admistration whatsoever.