Problem was solved by following code:
Public Sub PopupEditorMethod(ByVal sender As Object, ByVal e As ExecuteCommandEventArgs(Of OurObject))
Dim row = CType(e.OriginalSource, Xceed.Wpf.DataGrid.DataRow)
row.EndEdit()
'popup implementation
End Sub
We cancel the rowediting of our cell's parent row. This makes sure we don't have any inconsistent values.