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As mentioned in the thread above I was working on the same issue. Our solution has been to add a custom section to the start of the DCT (BOOTLOADER_SECTION) which we controlled so this contains the data required for our bootloader to run. The bootloader is only allowed to look in this section. The cost of doing this is that we need to modify the DCT functions to support this new section and to ensure we do not get into problems if the DCT API changes, the bootloader has its own DCT functions.
This has worked great since we patched our 3.1.2 based devices.
Yes, we're running custom DCT code patched on to the WICED code, my hope was to avoid re-patching with 3.6.3, since a DCT upgrade path was promised here--but I'm not sure it will come through.