When practicing EMDR you will still encounter problems generic to therapy. If a client has not been properly prepared, and unresolved secondary gains exist, resistance to change can cause additional tension which may result in a headache. However, two days is most uncommon. Headaches can be a sign of dissociative disorder, so appropriate diagnosis needs to be made. If you suspect that eye problems can be a factor than make sure you use handtaps or tones instead. And sometimes there are simple coincidences. Is there anything else going on that could have precipitated a headache? Is there a history of migraines? If so, use the appropriate history-taking and procedures to directly address this problem.