I have many books with accented characters, mostly in authors' names, and have never encountered any issues with either calibre or with various readers and reading apps.
I suspect that the OP's issue is the result of the PDF to HTML converter's (tagged as pdftohtml 0.36 in the metadata) failure to handle the PDF's font encoding properly, either putting a bogus character in place of the umlauted character or in specing the HTML output with the wrong encoding leading the HTML to EPUB conversion to go astray.
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