I came here and created an account JUST to report this exact same thing.
Got my first mystic syrup, created a totem using the tool bench, discovered that the syrup stayed around but multiple items in the same chest as the syrup had disappeared (all my sea/cave/river jellies and hardwood, plus more that I don't remember).
I went to create more totems and more stuff kept disappearing, so I'm just selling my syrup now because I'm scared to lose more items. The syrup was never consumed by the crafting recipe.
I'm on the Switch one, latest update, year 4.