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I would personally opt for the new 2012 R2 VM, and then perform a PI migration and upgrade. A key reason for this is you have an easy rollback option should something go wrong during the upgrade. Granted, you stated the server is part of a PI Collective, so you already have an option for continuity in the case of a mishap. But the new VM also allows you to have a 'clean' server again, and it's not really that difficult or time consuming to migrate PI to a new server. And if your system managers are willing to provide support such as server renames, or IP address retention, or DNS aliasing etc to allow clients and interfaces to connect without having to update each client computers KST, then a switchover to a new VM becomes less of a hassle.
All of the customers that I have worked with over the past several years have taken this route of moving their systems to new VM's when an OS upgrade is needed (or taking this as an option to go to the newer OS when a PI system upgrade is wanted). I've migrated and upgraded several PI systems this way, and found it to fairly straightforward. Unless your server is running some piece of legacy software that you don't have installers for, or is difficult to install and configure on a new server, or a similar kind of situation, then choosing an in place OS upgrade doesn't seem to make a lot of sense when spinning up a new VM takes little to no effort.
I don't have any direct experience with upgrading the OS on a PI server, but I shouldn't think there would be any side effects on PI from an OS upgrade. For me though, the appeal of a nice clean server build to start with trumps upgrading Windows itself on an existing server.
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I agree with John Messinger, a move is preferable to an in-place upgrade, especially if the server has been in service for a few years. You have the advantage of being able to fall back to the untouched old server if the upgrade goes awry, and you get a fresh new server that you can have at the current corporate standard.
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I second John's and Steve's reasoning on just migrating to new hardware (or VM). I also want to generally caution against doing an in-place OS upgrade for another reason: there can sometimes be compatibility issues between certain versions of PI Data Archive and certain versions of Windows. Although rare, we did have one occasion when PI Server (Data Archive) 2012 was released, where it was unable to perform a VSS backup on Windows Server 2012 R2. In this scenario, if you were to upgrade the OS without the necessary resolution hotfix, the PI Data Archive would not be able to run any VSS backups. So even prior to migrating to a new OS, I would recommend checking that the OS is indeed supported by the version of PI Data Archive, and also check the alerts/known issues on our Tech Support site to make sure there aren't any bugs or issues which may affect you.
As Steve and John mentioned, it's always a good idea to have a rollback option, in case things go wrong!