You must run the NKitProcessingApp.exe, then change the mode to "Convert to ISO", then uncheck the "Full Verify" option.
Then import your .nkit.iso file, click in "Process" and let it do its work.
To ISO: .1.2.3.4.5.6.7.8.9.10 ~ 0m 31s [MiB: 4482.3] NKit Invalid
|DETAIL
|...............................
|!! Update partition *_E0F6F63D missing - Adding filler. It may be Recoverable
|...............................
Verification Failed Crc:3BD04A8D - Failed Test Crc:8C30D1D7
Deleting Output
@E6903
You need to download the nkit program with the partitions included otherwise the process will continue to fail because it is trying to rebuild the ISO with the missing partitions and if it does not find them it gives that error.