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The custom metrics are stored in the data repository database (RedGateMonitor). So if you are reusing the same database (or restoring a backup of the database to a new location and using that) then the custom metrics will be preserved.
Alternatively you can using SQL Data Compare to deploy the following tables from the old database to the new one.
settings.CustomAlertDefinitions
settings.CustomMetricClusters
settings.CustomMetricGroups
settings.CustomMetrics
settings.CustomMetricSQLServers
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If you uninstall and reinstall a version of Redgate Monitor will you need to re-create your custom metrics or will they be carried through?
If they are not saved, is it possible to export the metrics and re-import them?