So I opened the annotated PDF to another viewer, where it appears OK, and then reinserted it as attachment in Evernote, but it again appears corrupted.
Even if it worked that was, it is a workaround, so I could just use an external PDF editor anyway and spare the trouble.
PDF management and annotation has worsened in recent versions of Evernote, to the point that is basicalle is unusable. Let's hope the new owners will give this feature some love...