Talk sternly to them, and deprive them of sweets
Canning & Food Preservation
Canning and preserving food. Includes dehydrating, freeze-drying, etc.
Next question: what can I use depressed apples for?
Nothing, they just sit there.
I think this is mostly dependent on the type of apple you used. Some types withstand the cooking better and can stay more firm!
Calcium Chloride is generally used to strengthen pectin in canned goods. I have no experience in canning though, I don't know what changes it would bring.
With fresh apples I usually mix lemon juice with a teaspoon of cornstarch, toss with the apples, let sit 20 minutes, then cook. Acid firms pectin, Bases (baking soda) breaks it down (and lowers the temp for Maillard reactions, good for emergency Onion Confit at the expense of texture).
Calcium Chloride is what makes many commercially canned chopped/ diced / whole tomatoes suck for anything but salsa, no matter how long they are cooked they do not break down.
You could try a bit of your favorite acid to see if it helps.
What purpose does the cornstarch in your recipe serve?
It initially helps it adhere to the Apple pieces, sorry I wasn't very clear. I toss the pieces with cornstarch, then add the lemon juice. After it is brought off the heat it acts as a thickener.
If you do not need thickening then omit it, I leave it out at Thanksgiving when I use apples for stuffing.
I don't know how acid would change things post canning, I would think it would still firm pectin though, so it might be worth trying.
As I understand it Calcium Chloride is used commercially because it does not change acidity levels, and it adds salt. It is very 'salty' but does not increase NaCL (sodium) levels.