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.
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