"If you need more information go to the fare rules on our website" is "call center english" and means in plain english: "I have absolutely no clue, please don't ask me more questions about this"

For complex matters like this, I'd suggest to ask them by e-mail as this will give them the opportunity to double-check everything.

A through fare can only have one set of rules, and if these rules say "no penalty" there will be no penalty. A partial refund would not be possible without recalculating and reissuing.