No, not a problem. I'd rather not go through everything only to find they were behind a locked door or something, too (which it isn't).
First, a fairly large portion of the workforce was entirely idle, and most of those had all hauling labors enabled. The items at the shops themselves do not have the "tasked" tag attached to them.
The stockpile itself has everything but clothes, armor, backpacks, quivers, splints, and crutches enabled. Those have their own stockpile, which has its own private but different issues. No changes were made to materials or quality.
The items themselves largely fall along the lines of "microcline bracelet" and "turtle shell figurine of dwarves," so they really should be moved. What's more, up until now, they were moved into the stockpile, but now all that's there is a legendary artifact (a palm earring). Note, it's empty because I just traded basically everything that was in it.
An interesting point in that was that when I was designating things to be moved to the depot, the items in the workshop appeared, and the ones that I designated to be transported to the depot were quite promptly, thanks to the fair number of idle dwarves.
The workshops are within the safety burrow, as well.
Feel free to ask any of the things that I could have done that were just incredibly dense. I'd be perfectly happy to find that this was my own error...