Is there a way to Upgrade my ESX 4.0 hosts to 4.1 with the Update Manager from vCenter Server?
No, this package is for manual upgrade only and you don't need it with Update Manager.
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MCSA, MCTS Hyper-V, VCP 3/4, VMware vExpert
Yes, you need to upgrade vCenter 4.1 first and then just upload upgrade-from-ESX4.0-to-4.1.0-0.0.260247-release.zip package to upgrade manager.
All other steps how to upgrade you can find in Update Manager Manual.
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MCSA, MCTS Hyper-V, VCP 3/4, VMware vExpert
Do I have to deploy "pre-upgrade-from-ESX4.0-to-4.1.0-0.0.260247-release.zip" first to the ESX servers?
No, this package is for manual upgrade only and you don't need it with Update Manager.
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MCSA, MCTS Hyper-V, VCP 3/4, VMware vExpert
Thx!