Hi Dean,
You can remove products using the Remove button on the Preferences > CCS > RTSC > Products page. Physical removal of target-content products currently isn't handled by CCS. There is a work-item scheduled for CCS v6 to address this - SDSCM00047983 Moving/removing target-content products in filesystem puts CCS in a bad state.
For now, i would recommend re-installing your CCS v5 image to recover from this.
Thanks,
- Baltasar