If you store items in a workbench at one settlement and try to access those items at a different settlement that is not connected by a supply line then those stored items will be inaccessible. This is likely what happened, because I had a similar issue with turrets stored at The Castle being inaccessible from other settlements because The Castle was isolated from supply lines. Opening or reopening the supply line fixed the issue.
Alternatively, your items may have been scrapped for crafting other gear. If you stored some wood flooring and you later try to to build an item furniture that requires wood then your flooring may have been scrapped. I've not heard of that happening, but knowing Fallout's extensive bug list may be possible.