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Is it possible to export isochrone boundaries as shapefile?

Yes, this is possible in two steps:
1) Out of existing isochrones, create new POI area objects with the AddIn '2D-Isochrone -> POI':
Scripts -> VisumAddIn -> GIS -> '2D-Isochrone -> POI'.
2) Export these POI objects as shapefile:
File -> Export -> Shapefile