Just to share with you the general limitations and known issues on the Intel System Studio 2016 for Microcontroller for D2000 platform.
The use of UART-B or PWM0 signals will multiplex JTAG pins and therefore prevent further flashing and debugging of the board quark_D2000. To recover your board, the BSP-ROM can help - simply set IO0 pin to GND (Arduino RX or SoC pin13), power cycle your board, and flash again following steps of Deploying a project. After your board is recovered, just unground IO0.
By default, only the 4 HW breakpoints are supported. For that reason, limit your breakpoints to a maximum of three and remove unused ones. If more breakpoints are needed, SW breakpoints in flash can be used but be aware that stepping/resuming over breakpoints will be very slow and the more SW breakpoints you have the slower your debug session will get.To enable them, replace monitor gdb_breakpoint_override hard with set breakpoint always-inserted on while developing in GDB command line.If you are using Eclipse*, locate the following option from the toolbar menu: Run > Debug Configurations. Locate your project under Intel ISSM and modify the Initialization Commands section accordingly