Line a fine sieve with muslin and set over a deep bowl. Add yoghurt; fold up edges of muslin and tie a knot to secure. Refrigerate for 12 hours or overnight to drain. Transfer labne to a bowl; discard liquid; keep chilled until ready to use.
Place lemon in a saucepan, add enough water to cover and bring to the boil. Cover with a plate to weigh down lemon. Reduce heat to low-medium; cook until tender (1 hour). Drain, cool and chop, discarding seeds.
Meanwhile, preheat oven to 180°C. Spread out walnuts on an oven tray lined with baking paper and roast until golden (15-18 minutes); cool.
Grease a 23cm-diameter springform cake tin, and line base and side with baking paper. Process shortbread, walnuts, thyme and ½ tsp salt flakes in a food processor until finely chopped. Add melted butter and process to a sandy texture. Using a flat-based glass, press mixture evenly over base and up the side of tin; place in the freezer until base is firm (10 minutes).
Reduce oven to 160°C. Meanwhile, process chopped lemon and sugar in a food processor, scraping down side, until very smooth. Add cream cheese and 400gm labne; process until very smooth. Add eggs, one at a time, scraping down side between each addition until combined. Add flour and lemon juice; process until smooth. Pour mixture into crust and bake until filling sets around edge but centre still has a slight wobble (45-55 minutes). Cool
in oven with oven door ajar (2 hours). Refrigerate overnight to set completely.
For honey and thyme syrup, cook honey in a small saucepan over medium-high heat until lightly caramelised (3-4 minutes). Remove from heat, add remaining ingredients, swirling pan to combine (be careful, mixture will spit). Cool to room temperature.
To serve, place cheesecake on a large platter or cake plate, drizzle with honey syrup and scatter with manuka flowers.