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at least in the 10.x (and latest versions) there is a table in the database for AlertDefinitions and AlertActions. Verify they exist in your 9.x implementation and see what is in them. These should be safe during upgrades.
Before doing any upgrade, I recommend you do a full backup of your database prior to upgrade. Run your upgrade on the primary NPM engine and get in to see if the alerts/actions are there as they should be.
I did not have any issues when I did my upgrade from 9.x to 10.x that I recall.