The last type of nonvolatile information in flash is chip-level protection. This consists of one byte that restricts access to the chip’s resources (register, SRAM, and flash) by an external programmer or debugger.
Please check page# 7-8 and #43 of this doc:
Nonvolatile memory programming refers to the programming of flash memory in the PSoC® 4 device. This chapter explains the different functions that are part of device programming, such as erase, write, program, and checksum calculation.Cypress-supplied programmers and other third-party programmers can use these functions to program the PSoC 4 device with the data in an application hex file.
Please check this discussion , it discusses the limitation of Jlink to program hex file generated by PSoC Creator:
J-Flash should only be used with data files that solely contain (programmable) flash addresses.
This limitation comes because Jlink can't program Nonvolatile memory in the PSoC® 4 device
Please check page#211 of this document, as all system calls are part of Nonvolatile memory
So, it seems from all this above info that JLINK can't change the chip protection setting