Minecraft appears to use the pre-existing "burn timer" in furnaces when it tries to autofill a recipe that cannot be crafted (using the current timer that has been set for the current fuel and ticking it down, even when nothing is being smelted) and it does the item swapping thing all the meanwhile, for both the fuel slot and the item slot. (Screenshots provided.) After waiting a little while, I placed the item back in its slot, but the burn timer does not revert to the old value (when I clicked on the recipe entry)

This has happened only in creative mode as of the time I am writing this report, and I am not sure if this issue is reproducable on survival mode.

Edit 04/13/2018: Can reproduce on survival mode.

Reproduction steps (unsure):

1: Set up a smelting operation as you would normally (place items and fuel...)
2: Wait a little while for some of the items to smelt, but not long enough to the point that the fuel is fully used up
3: Open the recipe book and click on a recipe that you cannot craft yet

I would expect the burn timer to pause/stop when viewing an uncraftable recipe, but it doesn't seem to do that...