OK, solved this one as well… I’m good this weekend, ran into several issue and solved all of them in a coincidence 
The icons from all the different themes are still in place and yes, I now know where they are and if I replace the original images inside the themes folder they also change on the desktop but you need to be carefull, the full and empty bin are in two different location with the same name, only referred to via a symlink.
But this was not the problem, the problem was that the icon I set up myself as the last one (the empty one) is stored somewhere and I now know where. For those of you running into the same problem :
Inside your home folder there is a .nautilus folder. Below that one are some other subfolders and in one of those folders you’ll find an XML file with a very weird name but containing the word DESKTOP inside.
When I opened this file I saw that it contained the setup of my desktop, that is the list of icons, their size and location on the desktop. If you change the icon yourself, then it’s in this file that it’s stored.
My recycle bin was reconfigured like below (I’ve put the line in blue bold):
<?xml version=“1.0”?>
<directory><file name=“Vista.volume” timestamp=“1241340296” icon_position=“64,342” icon_scale=“1” icon_position_timestamp=“1241340296”/><file name=“trash” timestamp=“1241341546” icon_position=“64,762” icon_position_timestamp=“1241341546” custom_icon=“file:///usr/share/cairo-dock/plug-ins/dustbin/themes/Metal/trashcan_empty.png” icon_scale=“1”/><file name=“home” timestamp=“1241340296” icon_position=“64,102” icon_position_timestamp=“1241340296” custom_icon=“file:///usr/share/pixmaps/gnome-home.png” icon_scale=“1”/><file name=“Data.volume” timestamp=“1241340296” icon_position=“64,262” icon_scale=“1” icon_position_timestamp=“1241340296”/><file name="." timestamp=“1241340296” icon_view_layout_timestamp=“1241340296” window_scroll_position=“x-nautilus-desktop:///network”/><file name=“computer” timestamp=“1241340296” icon_position=“64,22” icon_scale=“1” icon_position_timestamp=“1241340296”/><file name=“network” timestamp=“1241340296” icon_position=“64,182” icon_scale=“1” icon_position_timestamp=“1241340296”/><file name=“PORTABLEAPP.volume” timestamp=“1241196788” icon_position=“64,742” icon_scale=“1” icon_position_timestamp=“1241196778”/></directory>
All I had to do was delete this part in the file :
custom_icon="file:///usr/share/cairo-dock/plug-ins/dustbin/themes/Metal/trashcan_empty.png"
Save the file, restart nautilus and there was my original icon from the current theme. All I had to do now was replacing the full and empty icons with my own files.
Now it works fine.