over the past week, I've had entire stacks of items just disappear during synths.
Synth 1: Converting newts to lightning crystals: I had 99newts and started with 1 lightning crystal. After using up all of the newts, and only having 7 breaks, I realized that I only had 54 lightning crystals. That's an easy 130 crystals LESS than I should have had.
Synth 2: making brimstone. 4pyrite make 1 brimstone. With 2 stacks of pyrite, I should have been able to make 49 brimstone. I had 2 breaks. After using up all 2 stacks of pyrite (according to my inventory and the craft window) I only had 17 brimstone.
Synth 3: Making cotton bolls into cotton thread. 2 bolls for 12 thread. I had 3 stacks of bolls which equals 1782 thread or roughly 18 stacks. After the game had said that I was out of cotton bolls, I check my inventory. There are only 10 stacks of cotton thread.
So..it seems that items are either just disappearing during synths or the game is actually using more of the item than it is recording because this shouldn't be happening =\