Similar to this question, I have some applications (Calibre, texdoc) open PDFs with Mendeley. Opening PDFs from Thunar, Thunderbird, Firefox etc. opens evince, the expected default.
It seems that those applications use
$ xdg-mime query default application/pdf mendeleydesktop.desktop
I tried to find where this comes from but was unsuccessful; I fixed it with
xdg-mime default evince.desktop application/pdf
The question remains: where did
xdg-open get the idea that Mendeley should be the default PDF viewer from?
I'm using Ubuntu 16.04 with i3 4.11.
xdg-open is at version 1.1.0 rc3.