It has happened to me a couple of times, that I was unloading stuff in a hurry into a chest and I inadvertently loaded a tool into it without realizing, and, since I didn’t need that tool until later and hadn't used it in a day or two, I didn’t have
any idea
which chest or where. Each fine I thought I lost it somehow but in the end, as Ereo said, you may need to look through every chest or loadable furniture everywhere (more than once even if looking too quickly), unfortunately (if the tool doesn't show up after you go to sleep that is). From what I learned from other's posts is, if it doesn't show up after going to sleep at night, it has most likely not been lost but put into a place with storage slots inadvertently (barring a bug) .
The looking is a complete pain, I feel your pain. Been there, wasted 2 days looking before I found it the last time. In the words of Homer Simpson: D'oh!