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CCS/LAUNCHXL-CC2640R2: Project menu options have disappeared?

Part Number: LAUNCHXL-CC2640R2

Tool/software: Code Composer Studio

I revised an example project, rtls_passive, which previously loaded and debugged fine, to use one antenna array as outlined in 

http://dev.ti.com/tirex/content/simplelink_academy_cc2640r2sdk_2_40_03_00/modules/blestack/ble_aoa/ble_aoa.html

Aftwards I get the following error when trying to load and debug automatically,

'Texas Instruments XDS110 USB Debug Probe/Cortex_M3_0 : Target must be connected before loading program.'

I can manually load and debug by launching from the ccxml file, connecting and then debug but...the debug menu runs but all break points are disabled.

How come I can't debug automatically anymore?

Thanks