Please open a ticket in your customer zone (if you are a paid customer) or alternatively on our public tracker (on GitHub)
There is simply no way you can backup a running VM with HDD in passthrough. Because you can't "snapshot it".
A working alternative would be to use the HDD as a local ext SR, and create a virtual disk for this VM. Problem solved.
edit: I move the topic in the XOA cat. Here is the XOSAN doc: https://xen-orchestra.com/docs/xosan.html