As I needed it urgently, I wrote a python script which remove the flag from the db with this command :

vdi_ref = session.xenapi.VDI.get_by_uuid(vdi_uuid)
session.xenapi.VDI.remove_from_sm_config(vdi_ref, "paused")

It worked and my vm are back to business!

@Danp Did you remember what command you used to remove the "paused" flag, as the link from Citrix is not working anymore? Thanks!