Here's a few tips regarding Alexa.
When troubleshooting, always use the Alexa app, instead of voice commands. This way, you are sure about what device is being controlled. When controlling via voice, Alexa may be confused with a device or room using a similar name.
If you find you have duplicates, you need to delete them from the Alexa app. You may be tempted to start fresh and delete your mappings on portal, but there is no need to do that. The only case where it may be useful is if you are mapping an ISY node that no longer exists on your ISY (or eisy/polisy).
When using V3, when adding/editing/removing a mapping, it should be updated directly in the Alexa app. There is no need for a device discovery. That's if the skill is linked. If you change your mapping while the skill is not linked, then when linking it will get discovered.
I don't think the problem you are having is the alternate spoken. Alternate spokens are treated exactly the same way as the primary name you gave. Using alternate spoken just creates additional Alexa devices mapped to the same ISY node.
One thing to watch for are Alexa scenes, especially if you had some when using V2. Alexa scenes are kind of hidden. So if you have an Alexa devices with the same or similar name as an Alexa scene, then Alexa will see multiple device with the same name. That's why it's important to first test controlling devices directly with the Alexa app - you know which one you are controlling.