Hi Libor,
I'll summarize my interaction with the tool below:
1. Open the tool
2. Set FlexSPI NOR - simplified using the AT25SF128A template, modify Memory size to match the memory I have (1 MiB), and click on Test. Log attached.
3. Click on "Convert to FCB". Operation fails - log attached.
4. Open Tools->Flash Programmer. The window says "Erasable block size: not known" and "Erased range: not known".
Modify the buffer size to match the memory size: 0x100000, and click Erase. The status is "Sucess: Erase memory region 0x60000000 - 0x600FFFFF".
5. Click on Black check - result is "Success"
6. Click on Read - result is "Success"
7. Click on "Fill...", specify patter "0xcafeface" (32-bit), and then Write - fails with message "ERROR: `blhost -- write-memory 0x60000000 1048576` >>> FAILED with exception: MBoot: WriteMemory interrupted -> FlexSPINOR: Command Failure".
8. Reset target and open the Flash programmer again, then read 0x100000 bytes. The Log window displays "ERROR: TAG does not match: fafecace"
9. Memory read is complete and buffer is filled. It appears that previous Fill operation succeeded in writting the first 512 bytes, but the pattern seem wrong. Screenshot below

10. Click on Erase memory - result is Success
11. Reset target and open Flash programmer again. Read first 0x400 bytes - success
12. Try to write "0xcafeface" at address 0x0 and "0xdeadbeef" at the end of the 0x400-bytes block. Result is "ERROR: `blhost -- write-memory 0x60000000 1024` >>> FAILED with exception: MBoot: WriteMemory interrupted -> FlexSPINOR: Command Failure"
13. Try to read the memory again - nothing has been written.
14. Try to write the whole memory block at one go - fails with "ERROR: `blhost -- write-memory 0x60000000 1048576` >>> FAILED with exception: MBoot: WriteMemory interrupted -> FlexSPINOR: Command Failure".
15. Erase memory - success
16. Try to fill the first 0x400 bytes with 0xcafeface pattern:

Operation fails again.
17. Read 0x400 bytes - success. The pattern seems shifted.

So it appears there's a problem with writting to the flash. Could that be the reason "Convert to FCB fails"?
I also can't upload application to the flash using JLink and MCUXpresso.