Web archives combine everything into a single file, and they also store the HTTP response data, so in practice they should never be identical even if you download the same page twice in quick succession.
Some formats like RTFD do store individual files like images as distinct files inside of a package folder. These will also not cause spurious duplicates because EagleFiler treats the whole package as a unit. It’s only considered a duplicate if the document and all the attached files are identical.
OK - thanks. I have seen sporadic duplication errors for JS and HTML fragments, so I’ll see if I can track the problem down - there may be some other cause. (I suppose an obvious one would be old output from “save as” from a browser - HTML + asset folder - dragged into EagleFiler at a subsequent date.)