Hi,
did you try to remove the Hooks "Reset entire System" and "Program FPGA" when running your application?
Like shown in the attached image or similarly here under Point 15. -> https://wiki.trenz-electronic.de/pages/viewpage.action?pageId=157219241
Also you can delete the content of your QSPI Flash per script typing "TE::pr_program_flash -erase" in the TCL console when using our reference design environment.
Or simply right-click in the hardware manager on the memory device "Program config memory device" and choose a random programming file and tick only the Erase box.
good luck!