Hi @filip091
Do you mean, you use the directly MIMXRT1060-EVK board, and that run the SDK code is OK, but your own code has issues with the flash, right?
MIMXRT1060-EVK board in default is IS25WP064AJBLE, and that works OK with our SDK.
About the flash programming, it is using the flashdriver with the IDE, so you can't find it in the app code.
If you are using the MCUXpresso IDE, the .cfx is the related flashdriver.

If you want to check the flash program and erase and read, you can download this code to the internal TCM:
\SDK_2.9.3_EVK-MIMXRT1060\boards\evkmimxrt1060\driver_examples\flexspi\nor
Then, debug it, you will find the details.
You also can enter the serial download mode, then use the MCUBootUtility tool to download it.
Tool link:
https://github.com/JayHeng/NXP-MCUBootUtility/archive/refs/tags/v3.3.0.zip
the related user manual is:
https://github.com/JayHeng/NXP-MCUBootUtility
Wish it helps you!
If you still have questions about it, please kindly let me know.
Best Regards,
kerry