Thanks Laura for your help. What I read on Seat 61 is that the train cancellation ended in 2017. So that didnt concern me. Unless he's wrong. The Greek Railway site doesn't address this and it looks like trains are running from what I see but other sites do mention it. (the bus transfer)
I was hoping someone who has tried to take it or has taken it would chime in here as this is an important gap for me. My other options are the train through Sofia to Belgrade (not so good connections for me) or the Ferry from Patras to Venice rather pricey at €500 with a cabin and my Pooch.
My real end destination for this leg is actually Budapest.