Why did Cartoon Network never air the last four episodes of Zoids: Chaotic Century?
The Final Battle aired on 2002 May 2nd and almost a year later The Ancient Memory (1) aired on 2003 January 4th with the other three episodes. It is possible that Cartoon Network did air the last four episodes, or that it was Network 10/TV3 in Australia/New Zealand, respectively.

There was definitely some sort of discrepancy that prevented Zoids: Chaotic Century from being shown from start to finish. Sadly, the only people who can answer this question are those that worked at Cartoon Network at the time.