the vSE gets placed in any available System vDC. It's also not considered part of the vApp for the purposes of the API (from what I recall) ... more like a feature of a network. But I don't know if the vApp Network instance even provides you the data.
what you could do.
locate the VMs in question invCenter, then find the isolated port group.
once you have the isolated port group, find the vm with the vse-.... name attached to it (if it exists)
vmotion the vse- to the other System vDC resource pool in the other cluster.
Maybe something like that could work?