Repost the question in the Calibre forum, if that's what you're using, Fermthe, and I'm sure that you will get a reply.
With a PDF file, you need to embed a Greek font.
The same is true if you are using Book Designer.
HarryT uploaded some Ionic Greek here:
https://www.mobileread.com/forums/showthread.php?t=12166
made in the days when he owned a Sony PRS500. He used Book Designer and embedded a Greek font.
I'm not sure how far Calibre supports font embedding, so suggest that you ask in that forum.