I found this post on Renntech: Soft top adjustment - 986 Boxster Top Issues and Solutions - RennTech.org Forums
That post suggests that you can adjust the rear main bow of the convertible top frame by turning the 14mm adjusting bolt Counter-clockwise. This seems like it could lower the rear main bow of the top and thus lower the entire top enough for the clam shell to close on top of it.
Of course it could also bust the rear window.
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2000 Arctic Silver/Black, Hard Top, On Board Computer
PNP Rear Speakers, HAES 6-Channel Amp, Avic Z140BH,
Painted Bumperettes, 2004 (OEM) Top, Homelink integrated in dash with Targa switch, 997 Shifter, Carrera Gauge Cluster with silver gauge faces, heated 12-way driver & 8-way passenger seats, Litronics, silver console
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