When tearing down a wall, I removed two, connected baseboard heaters, installed a junction box and ran the wire under the new floor (I would say the junction box is now unaccessible). Power to both the thermostat and the heater wiring was tested good and I tried both a new thermostat and a new heater. The thermostat clicks but the 'heater on light' does not go on and the heater does not work. When I disconnect the thermostat I get power in the black wire but not the red? Whwn I disconnect the heater, I still have power in the thermostat. The place is new to me so cannot say for sure how it is wired but I would have thought power source to thermostat to heater.

I am lost as to what the next step is?

If you don't have power in the red, as noted, you don't have 240V, an probably a disconnected wire, but did you check the power at the breaker? Making the Jbox inaccessible, an NEC code violation by the way, is never a good idea, how will you check the wire connections? If you can get to the box, in whatever manner, put the jbox in the wall and use a blank cover plate.

Power is fine at the breaker - but 110v not 220v. The old baseboards worked fine with this power though (again, this is a new property to me). The (waterproof)Jbox is "accessible" but in a very small crawl space under the floor (no other option with only a short wire to work with from the wall that was removed and old baseboards disconnected). If there was a disconnect here I would not have power at the new wire? So, old baseboards worked fine - the only change is the Jbox and extension over to the outside wall of the wire from the thermostat. Am I missing something?

That is considered accessible. I quess my question is, if you have black and red, what is the purpose of the red wire? "power in black but not red" It is not connected to a breaker? Did they use a recoded white for power? What are the voltage requirements on the heater and what is the wattage of the heaters? How many wires on the t'stat?
As a general rule, 2 strip heater on 1 line are almost always 240V, 2 hots and no neutral. Hot black, hot white to the 2 red t'stat leads, 2 black out of t'stat to black and coded white to first heater and then 1 black and 1 coded white to second. You could have a 3 wire, black and red hot but the white would just hang. Grounds all the way through. Tell us a little more, some confusion exists over what wires you have to the t'stat.