Blend until smooth 3 eggs, the flour, milk, melted butter, and salt. Cover and chill batter 15 to 30 minutes.
Melt 1/2 tbsp. butter in a large nonstick frying pan over medium-high heat. Add spinach, season with salt and pepper, and cook until spinach is tender, 3 minutes. Scrape into a bowl; wipe pan clean.
Whisk remaining 2 eggs in a bowl. Stir in cheeses, chopped thyme, 1/4 tsp. pepper, lemon zest, and spinach. Set aside.
Heat pan over medium-low heat and brush with butter. Add a scant 1/4 cup batter and tilt to cover bottom. Cook until almost set, about 30 seconds. Flip and cook until crêpe lifts away from pan edges, 30 seconds. Transfer to a plate and repeat to make 7 more, stacking as you go.
Spoon about 2 1/2 tbsp. cheese filling along the lower third of top crêpe. Fold crêpe to seal, tucking in sides. Set blintz aside, seam-side down. Repeat.
Melt 1/2 tbsp. butter in pan over medium heat. Cook 4 blintzes until browned, turning once, 2 to 3 minutes per side. Wipe pan clean and repeat with 1/2 tbsp. butter and remaining blintzes. Sprinkle with thyme leaves and serve with sour cream.