I think this is due to the 8M memory structure! I think the memory is made up of several banks [bank0 to bank7] and you probably patched only the bank0 !
If the active partition starts @ offset 0x4000 for the bank0 ... the active partitions for the next banks shall be at offset 0x104000, 0x204000, 0x304000, 0x404000, ..., 0x704000 ! the content of the 8 Banks must be consistent for the verification to be OK !
even if the flash chip state is unknown everything is booting but the thunderbolt still undetected