TC4x devices support two boot modes:
Below you can see the CPU Statuses in the Session Explorer window directly after reset in Foreground mode (CPU0 would be suspended with core synchronization enabled).

The difference between Background and Foreground Boot mode is important when programming or debugging.
If you issue a reset, you can debug the code as it is from the start, including the release of CPU0 by the CPUcs.
Programming Non-Volatile Memory (NVM) requires both cores to transition through the boot sequence correctly. Standard programming is not possible without help. winIDEA uses a Handshake script to ease the workflow.
The Handshake script emulates the handshake normally performed by CPUcs, allowing CPU0 to complete the boot process so programming can proceed.
1. Open CPU Options | Reset| Before Programming
2. In section Initialization before Programming | Initialize, add a custom script Fake finished foreground boot.
3. Enable Reset CPU after Download.
4. Perform Download.