There are two potential sources of your problem - (1) The control box under the driver's seat, or (2) As, you suspect, the memory buttons in the door sill. I think the problem is more likely to be caused by the memory buttons. I say this because it appears that the memory function works. It just won't accept new coding. Also, the location of the memory buttons (in the door sill) seems to make them vulnerable to water intrusion.
I suggest that you remove the memory control from the door sill and spray electronic contact cleaner on the control to see whether that solves your problem. If it doesn't, you can consider buying a used one from a salvage yard or the auction site.
If you decide to replace yours, please note that the early cars (like my 2000) had cable releases for the trunks. By 2002, Porsche had upgraded the trunk releases to electronic controls. If you buy a replacement double check to ensure it is the right one for your car.
When I removed the memory control from my door sill, there were three round plastic plugs on the inside of the door sill that cover the access holes for the fasteners that hold the control unit in place. I popped the covers off with a screwdriver. Then I inserted a hex socket into the holes. If I recall correctly, it is the 5mm size. I loosened the fasteners enough to free the unit and pulled the control unit up. Your car may be slightly different since it is newer, but I expect the removal process will be similar.
Good luck.
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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 997 adaptive sports seats, Litronics, silver console
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