Chocolate – I refrigerated fresh baked chocolate chip cookies over night. Will they recover

Preheat while doing other things. That's not a step that should take any effective time.

Don't measure so obsessively. Unless these need to be immaculate cookies, just accept a little variety. Scoop roughly with a spoon, or just your hands, and form into balls with your hands if necessary. If you desperately want precision, you could use a cookie dough scoop. But 56±3g sounds kind of over the top to me. Given that you said this is the main time sink, I'd suggest loosening up a bit.

Are you filling your cookie sheets fully? Do they fill your oven? Following a recipe's instructions to the letter, baking only 9 per sheet, is obviously the wrong thing to do if your cookies or baking sheets aren't the same sizes as those in the recipe. Note also that if you have many cookies per sheet, you can often fit more by tiling in triangles instead of squares.

And finally, reconsider your recipe. I'm sure this one is great, but keep in mind that most standard chocolate chip cookie recipes bake at 350F or 375F, and times more in the 8-12 minute range. If your recipe gives you exactly the cookies you want, and others don't, then stick with it, but if you're unnecessarily sticking to a recipe, try something else.

Edit: one more thought! Chilling the dough is probably important to your recipe, but you could measure/scoop while it's warmer and easier to work with, then chill in balls, and do the final forming once chilled.

And another, having seen your comment: given that you increased the baking time upon filling up the oven more, and are using insulated pans, you might actually want to increase the temperature to 350-375F and see if you can get back down to the 15-18 minute baking time. They may end up closer to the originally-intended consistency!

The resting is probably to hydrate to the dough, which will inhibit spreading. See https://cooking.stackexchange.com/a/29298/14401.

The bringing back to room temperatre is probably for one of four reasons:

• To help ensure you are baking each tray at a consistent temperature
• Colder dough will cook on the outside a bit more before cooking through, so they may brown or crisp or dry out more than is desired before being cooked through
• They might be somewhat easier to scoop at room temperature
• The original recipe author was just used to doing it that way.

It is highly likely that by adjusting the baking time slightly, you could bake them from refrigerator temperature, with only a very small change in quality. You would just have to try it and see.