I've create an PDF form using LibreOffice 5. For this document, the first form element refuses to turn up filled when filling + flattening using PDFBox 2.0.9 als well as trunk (512d016ad08a70dfb512f99d54092f8b586e8345).
It turns out that resolveNeedsTranslation does not encounter any PDFormXObject for the first element of this pdf form element but still returns false, although translation is still needed.
I've created a patch in https://github.com/michael-dev/pdfbox/tree/bugfix/flattenCorrectly .
I used evince 3.18.2 on ubuntu xenial as pdf viewer. Please see attached example pdf form and the different results using pdfbox 2.0.9 and with the above patch applied. The code used here is in example.java.