In Audiobook Builder, entire file names (with no tags being considered) get used for the Chapter names. Also, nothing actually gets cut off in the names, although what's displayed in the Chapters section view can get obscured by the window's bounds—if you stretch your window or double-click the name as if to change it and move through the text with the arrow keys, you'll find that a really long name goes on and on beyond what you see. So, in your case, the numbering would've been maintained, but you won't ever see the numbers later in iTunes since iTunes has its own Chapter name display limit. On the iPod/iPhone, though, you can tap on a Chapter and hold down to reveal a really long name.
Anyway, in tests, we found that iTunes won't show Chapters that use names of 499 characters or more and the same thing goes for iPod Touches and iPhones running iOS 6. So, it's particularly strange that you were seeing the Chapters in iTunes but not on your iPod. If you've kept up with your files in their original state, would you send several of them to us at
support@splasm.com? We'd like to test with them here.
Now, when it comes to dealing with inordinately long file names in the future using Audiobook Builder, we'd recommend using a batch Rename. For that, select all of the Chapters, choose 'Rename...' from the Audiobook menu at the top of the screen, and then use the tokens to setup a new custom naming scheme. For example, if you typed "Chapter " and dragged in the blue bubble [Chapter #] token after it, you'd end up with your selected Chapters showing as "Chapter 1", "Chapter 2", etc..