use_instance_uuid is intended to use the specific UUID of each virtual machine, as opposed to using a 'generic' UUID as the vmware probe did in the past. So if these UUIDs are indeed duplicates across machines this would be expected. (duplicate UUIDs are common when cloning VM's instead of creating them anew.)
In the past we have seen issues where VMs from different data centers were identified using a UUID of '0' and would trigger these alarms - so we added use_instance_uuid to be able to track each virtual machine separately by its own UUID -- so for this to work, the UUIDs must be unique for each VM.
So in other words this is working as designed, it is complaining because it is seeing more than one VM with the same UUID.
The solution here would be to get the VM's to get unique UUID's.
See the following.
Change your VMware VM UUIDs to be Unique
That being said, there is an existing feature request, to get the UUID to be actually specified in the alarm message. (currently no ETA.)
If it helps to lower the severity of the message, you could use a nas pre-processing rule change the severity of the message, e.g., lower it.
As an example, simply add a Script under Auto Operator->Scripts and save it as "lower severity of an alarm"
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event.level = 4
event.message = "my_message" (or some message you want it to filter on)
return event
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Don't bother testing it using the green arrow (Validate and Execute script) as it wont work and it will return an error if you try to test it in the AO window.
See attached screen shot for sample pre-processing config where the filter type is custom, and reference the script you just created. Name your rule "lower severity of an alarm" or something like that.
Then use the nas Status window and rt-click and send a test alarm with Critical severity (level 5) and message like "Test message from steved"
And you will see in the alarm sub-console window (filter on the message /.*steved.*/ and Apply the filter so you can see it easily among your alarm message), the alarm will automatically be changed to a major severity. (level 4).
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