Sure - it’s just another Powershell 1 liner:
Invoke-Command -ComputerName "EpicorAPP01" -ScriptBlock { Stop-Service -Name "EpicorICETaskAgent3.2.300.0" }
So you’re actually stopping the Task Service, and not specific Task Agents.
Does this run the risk of interfering with anything on the other Apps (like the Live one that was copied)?
Correct, it’s stopping the service and therefore bringing down all Task agents for the apps hosted on that server. There are no processes configured to run at the same time, and the factory staff that would be working at 1am when it processes this SSIS package wouldn’t be doing anything that requires task agent.
I’ll check the help files in EAC, there could well be a script to stop just my MRP task agent.
Sounds like Mighty Car Mods Unicorn Circuit 
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Take a look at your [Ice.ExtServiceRegistration] table. I think you might want to clean up any references to your production task agents. Personally I’d be inclined to delete the task agent on your destination app server and add it back again after you’ve done the restore. It makes me feel uncomfortable having any reference to production environments in a test/dev one. As always happy to told different.