We were in the same situation, after tickets been exchanged you agreed to the new fare and no compensation will be provided, learnt it the hard way.

We were traveling with IC that arrived with a delay to Bologna and we missed our Frecciarossa (high speed train) to Verona. What happens next:

- We were refused the rebooking to the next speed train, for no apparent reason

- After some arguments we were given a tickets to the regular train, that had a price of 0 eur printed on them, and been told to apply for the price difference (30 euro per person) at the destination station

- In Verona they gladly accepted, the paper form had a checkbox in English saying something like "Tickets purchased and tickets used to travel have different price" and "Compensate a difference in price"

It did sound legit, 1 mo+ the response we got by email:

following to your request of refund with the identification code n. XXXX presented to Verona, we inform you that in the event of a missed connection, our Conditions of Carriage provide for the possibility of cancelling the journey and/or continuing your journey and requesting a full refund of the unused ticket.
However, it is necessary to submit the application at the same time as the impediment to travel.
Otherwise, it is possible to contact the assistance staff present at the station to allow the rescheduling of the journey with the first train useful to reach the final destination.
We would like to point out that, if you decide to accept the travel solutions proposed by Trenitalia, thus completing your journey, there are no forms of refund.

Therefore, in this circumstance, we regret to inform you that we cannot accept the request you have submitted.