Take it with a grain of salt, but I think bonds are usually managed as a whole rather than edited port by port in the UI. As far as I can tell, the supported route is from the network section in Xen Orchestra (the bonding part of the infrastructure docs is here: https://docs.xen-orchestra.com/xo5/manage_infrastructure#network-bonding), and on the CLI side, the bond commands are documented at https://docs.xcp-ng.org/appendix/cli_reference#bond-create (there's a matching bond-destroy command alongside it).
My honest guess is you may end up destroying and recreating the bond with the four ports you want to keep, since I'm not sure removing a single member in place is exposed anywhere, but I could easily be wrong.
If there's a cleaner way that avoids the recreate, someone will let us know.