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As Ben said, this can happen so get in touch with your therapist so s/he can help you with those emotions. It's natural to feel concerned because the reason you're doing the EMDR is to get rid of your unwanted feelings rather than have them come flooding back.
Ask you therapist for some techniques you can use at home between sessions so you can take control over those unwanted reactions. EFT is a good one.
As you felt so much better after the first session if you were my client I would want you to carry on with it so that you can have that good feeling as normal - but of course it's up to you.