I had something similar in my Miata plastic window after I lowered it incorrectly and let it sit for a while. It took several weeks in the up position for the deformation to go away but not completely. Very annoying, luckily I found a new top for $300 (with glass) and avoided the whole issue. I would take it to an expert who installs tops to see what he suggests. Perhaps you can replace just the plastic.
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GT3 Recaro Seats - Boxster Red
GT3 Aero / Carrera 18" 5 spoke / Potenza RE-11
Fabspeed Headers & Noise Maker
BORN: March 2000 - FINLAND
IMS#1 REPLACED: April 2010 - NEW JERSEY -- LNE DUAL ROW
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