Using Logical Built-In Self Test (LBIST) can cause unexpected resets of the CPU, which disables debug communication and deletes all breakpoints.
Enable option Quick LBIST detection in Hardware | CPU options | SoC.
Quick LBIST detection means that debug status will be checked every ~20ms, which enables faster debug communication reconnection and breakpoints reapplication after LBIST resets the CPU. Note that after LBIST and CPU reset BlueBox requires a certain amount of time to identify that reset occurred. That means that before breakpoints are reapplied, the CPU is running without active breakpoints. In addition, the start of the LBIST must be executed while the CPU is running (e.g., not in a single stepping). In case you are using breakpoints be aware that before run, winIDEA always executes one single step, therefore breakpoints must be set at least 2 instructions before the start of LBIST.