Soops, I’m interested you say flue pipes get hotter than 250 deg, our stove pipe thermometer suggests the “best operating range” is 125 to 250 deg, and that 300 is “too hot”. Do you mean flues can get a lot hotter than that, rather than regularly burn hotter than 250?
OP, we used fire cement, which is prone to cracking as its hard to get the cure right (it wants to dry slowly with heat over a few hours) but had ours signed off today. Assuming it is the compound that is smelling, why not leave it as is, perhaps slowing the burn down, and get yourself some smoke pellets? Then before you next light a fire, you can use the smoke pellets to check the compound has sealed, and if not, you know you’ll have to re-do it with fire cement.
And as has been said, get a CO alarm, just incase.