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Stripping the paths from the hrefs appears to be intentional. There is an open issue about it that has a fix, but more time has to be spent looking at it to make sure it doesn't cause more problems than it fixes. Correcting links after splitting/merging should be fixed in the new beta.
But a simple link to a fileless anchor in the same file should work fine. What do you mean by "doesn't work"? What does the code for the link look like? What does the code for the anchor look like?
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