401 error in my API endpoint, if I don't set a new app token and connect-UAServer

If you’re on 2.5.5, you can actually simplify this and remove the use of app tokens. We added an -Integrated switch to some cmdlets to make executing jobs easier from APIs and dashboards.

No need to call connect or setup app tokens.

Invoke-UAScript -ID $script.ID -FileName "$SessionId.csv" -Integrated | Tee-Object -Variable | Wait-PSUJob -Integrated

$Pipeline = Get-PSUJobPipelineOutput -Job $Job -Integrated
$HostOutput = Get-PSUJobOutput  -Job $Job -Integrated

$HostOutput.Data
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