I added this issue to IA-upload tool on github:
https://github.com/Tpt/ia-upload/issues/14

Unfortunately, the new PDF > DJVU conversion is useless, as it loses too much quality.
Can we find a solution?
The IA-Upload tool is a great asset for the whole international community,
and it's very simple to teach librarians to upload stuff on IA and then use it to port it on Commons and Wikisource.
But when they upload new stuff on IA, we don't have the IA djvu anymore.
So the tool converts the original PDF to a new DJVU, and this is the part of the process that is failing.

I can think of 2 solutions:
* integrate this script from Alex brollo into the tool: https://it.wikisource.org/wiki/Progetto:Bot/Programmi_in_Python_per_i_bot/jp2todjvu.py
the script creates a good quality djvu
* have a toggle/top-down menu which allow the user to use directly the PDF.

Andrea