Verify that your notification scheme is correctly configured to receive only one notification (https://confluence.atlassian.com/display/AOD/Configuring+Email+Notifications). Is it one project that is giving you multiple notifications or more than one? Also make sure there hasn't been any changes to the active workflow on the project that includes firing a notification for transitions or changes.
If you can verify everything is configured correctly, then it may be best to file a support ticket at support.atlassian.com. This way we can enable debugging on the email handler and see why it is firing out multiple emails for all the updates in the project.
It's also possible this is appending to an existing email thread - when I get notifications in Gmail I find that it's often a thread of multiple notifications from the same issue/event. Not relevant if you're getting distinct emails, though :)
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