It could just be the end of growing season. Here in zone 8 ( East TX) the sweet gums are dropping leaves and the sour gums have many red leaves ; our temperatures are typically in the 80's and it has not been dry.
I am a big fan of drainage around the house but it's a challenge as water will go where it wants to go.
Yes, if you backfill with gravel and top with more landscape fabric to keep out the soil then turf it will drain better for the area on top of the French drain.
I suggest using a level to see where the slope is. Laser levels are readily available and if ...
The apple tree will have been using some of the water for itself, so removing it would mean there is now more free water, which might have increased the flow you notice. Otherwise, perhaps you have had an increase in rainfall generally.