In a large skillet, heat 3 tablespoons oil and add onions.
Sauté until soft, about 10 minutes.
Transfer to a bowl.
Add bacon to pan and sauté until fat is rendered and bacon begins to brown, about 3 minutes.
Using a slotted spoon, remove bacon, leaving behind as much fat as possible.
Add bacon to onions and set aside.
In a freezer bag, mix together flour and pumpkin pie spice.
Add 3 chops, seal and shake until chops are coated.
Shake off excess flour and place chops on a plate.
Flour remaining 3 chops and add to plate; reserve spiced flour.
Return skillet to medium heat.
Add chops 3 at a time, searing on both sides then transferring to a plate; reserve oily skillet.
Peel, core and cut the apples in two.
Slice each half into thin wedges.
In an ovenproof pot (preferably glazed ceramic) 8 inches in diameter and 5 inches deep, layer ingredients compactly as follows: a layer of onions and bacon, 3 chops, a layer of apple slices, some more onions and bacon, the final 3 chops, a layer of apple slices, remaining onions and bacon, and a final layer of apples.
Add spiced flour to oily skillet.
If pan is dry, add a small amount of oil.
Place pan over medium-low heat and whisk flour into oil to make a smooth paste.
Slowly add apple cider, whisking until smooth.
Bring mixture to a boil, then pour into pot, letting it filter slowly to bottom.
Cover pot with a lid or waxed paper and foil.
Place on a baking sheet.
Bake until chops are tender and apples are very soft, about 3 hours.