I refrigerated fresh baked chocolate chip cookies over night. Will they recover?
The reasons I know of to avoid refrigerating cooked cookies (there may be more):


Odors: If there are stray smells, like savory aromatics, the cookies may grab these and hold them.  Some may dissipate, but in general, if you absorb unwanted flavors you are stuck with them.
Hardness:  Chewy, jelly, candy, and oily cookies may turn hard when cold.  This might well apply, but should normally go away when you return to room temp unless it causes something to actually set up.
Chocolate Bloom: Chocolate that has been heated, cooled, change humidity, etc. can be subject to bloom, discoloration from sugar crystals forming.  You all three of those with fresh baked to cold chocolate chip.  It might not occur that fast and you might not even notice it for cookies, but I have certainly seen it in fudge for instance.  Mostly just unsightly though.
Moisture: This is a bad one for cookies and will be worse if they are not fully cooled before going to cold.  But even going from room temp to cold you are likely to get condensation giving you anywhere from a cooking that may stale more quickly to one that is soggy.  This one is unlikely to be fixed and would seem like the biggest caution.