Thanks Patrice - this works great. One change I had to make was to hide oAxes[3] on the first plot, prior to creating the second plot. Otherwise I get both sets of the ticks on Axis 3. other interested users see below:
; Create first plot
iplot, flux_data[1,*], color=[0,255,0], thick=4.0, ytitle="Flux Data", /insert_legend, $
name = "GPP", view_title=string(site_ids[i]), /NO_SAVEPROMPT
; Hide oAxis 3 on first plot
IdTool = IGETCURRENT(TOOL = oTool)
oWindow = oTool->GetCurrentWindow()
oView = oWindow->GetCurrentView()
oLayer = oView->GetCurrentLayer()
oDataspace = oLayer->GetCurrentDataSpace()
oAxes = oDataspace->GetAxes()
oAxes[3]->SetProperty, /HIDE
oAxes[2]->SetProperty, NOTEXT = 0, TEXT_COLOR = [0,255,0]
oTool->CommitActions
; 2nd plot with its own data space (so its own axes)
oCreate = oTool->GetService("CREATE_VISUALIZATION")
oDesc = oTool->GetVisualization("DATA SPACE")
oCommand = oCreate->_Create(oDesc, USER_INTERFACE = 'None')
iplot, vod_data, color=[0,0,0], thick=4.0, /overplot, Ytitle="VOD", /insert_legend, name = "VOD 10GHz", /NO_SAVEPROMPT ;linestyle=2,
; hide oAxes[2] of the new data space
oWindow = oTool->GetCurrentWindow()
oView = oWindow->GetCurrentView()
oLayer = oView->GetCurrentLayer()
oDataspace = oLayer->GetCurrentDataSpace()
oAxes = oDataspace->GetAxes()
oAxes[2]->SetProperty, /HIDE
oAxes[3]->SetProperty, NOTEXT = 0;, TEXT_COLOR = [0,0,0]
oTool->CommitActions
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