Dh and I were going to fly through MIA to STT in May but we had JB travelbank credits to use up so instead we booked through FLL which has us on JB from FLL-SJU-STT. The connection wasn't a biggie until I really looked at what we had booked. This was a built connection on the JB website and not something we put together ourselves. The flight has us arriving in SJU at 1:45pm and connecting ( ?) to a flight leaving SJU to STT at 2:27pm. It's been a number of years since we've flown through SJU but unless things have changed (an incredible expectation) there is no way if both us and our luggage have to move that we won't have some sort of hiccup.

Im guessing that perhaps this is simply a 1 stop flight although not listed that way which would make far more sense. I cant imagine JB would build it this way unless Im right. I called JB but the agent said it may or may not be...she couldn't tell but told me we had "plenty of time" (which is when I knew she had never flown through SJU). Is anyone aware of how I can determine if we're on the same plane from FLL- SJU and SJU-STT ?

You can see what's happened in the past on flightradar24 - find a previous inbound flight with the same number then look at the flight history for that aircraft's registration to see where it went next.

A cursory look shows that FLL-SJU typically flies on to MCO. So you're unlikely to connect on the same aircraft.

Even if it were the same aircraft, likely everyone must deplane anyway.

So I checked it out and apparently we do have to change planes in SJU. That gives us a grand total of 47 minutes to connect. We aren't kids and don't relish running from gate to gate and JB apparently only has 1 flight daily from SJU to STT with the other connections for the day being on Cape Air.
Will JB protect us on Cape Air if we don't make it? Would they likely let us rebook a split connection flight ie: out of FLL or MCO the night before to SJU or would they likely charge us the change fee since we were silly enough to book this in the first place (although it was offered on their website but I should have looked more closely at the connection) ?
Or does everyone think Im worrying over nothing?

The JetBlue connections are pretty easy to do. The mainland to Cape Air connections are REALLY long. You are walking across the ENTIRE airport to the D terminal gates for the Cape Air planes.

Map of the airport.

See above picture. A8 is the 321 arrival gate. D terminal is for Cape Air.

I made the fastest connection of my life to jump ahead to an earlier departure (25 minute connection) in August by running full speed across the terminal and made it with 3 minutes to gate close.

Did you have checked bags ? Do you think it is likely that our baggage will make it with this connection?

No, I didn't. If you are checking bags I would consider switching your flights. Island time, a 45 minute connection and checked bags do not mix in my experience.

I'm not everyone, but I do think you're worrying over nothing.

Assuming both are JetBlue flights (and not CapeAir), which is what you originally wrote, your max connection distance is incredibly close as JetBlue consolidated operations into the renovated A concourse a little while back. End-to-end is 1,000 feet. Even if you're the last off the plane it shouldn't be a problem.

Worrying about running to the other side of the airport is silly as you're not going to be doing that.

Originally we were flying from BUF-BWI-FLL-SJU-STT and overnighting in FLL. We've now changed our overnight to SJU (now BUF-MCO-SJU-STT and cut out one stop too ) still using banked credits on SW and JB and now have the overnight in SJU instead which means we don't have to worry. Thanks for the input.

I got to the point where I thought we would make it but I wasn't convinced the baggage would, and the next day we would need gear for our excursion....so didn't want to risk it.

Bags are more likely to make tight connections than passengers IME. A bag can be loaded well after the boarding door is closed.

Tell that to Swissport (who fortunately, does not service JetBlue as far as I know)

(I've had an experience where Swissport decided not to transfer my bags because they didn't think that they would make it, even though I made it!)