I disconnected the electrical plugs to both the actuators as per instructions on Alive Tuning website....
"It is recommended that you disconnect the electrical connector(s) from the EGR modulator(s), to prevent vacuum from being applied to the now
redundant vac hose(s). The engine management will then sense there is no EGR system fitted, so will disable any attempts of EGR operation."
http://www.alivetuning.com/alive-boutique/download/Td5-EGR-bypass-kit.pdf
This assumes you have correctly blanked the vacuum pipes.