I have a Windows 2012 R2 file server with about 2TB plus of data on it. My question is... can users work on the server during the virtualization process?
They can, but you will need to instruct them to save and close all open files/work on this server before the final synchronization begins and then not to attempt to work again until it's been brought up as a VM. It is no fun task to hunt and peck around a physical file server after it has been P2Vd to identify and manually move changed files.
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What are you using to perform this P2V?
Most modern applications used to perform this have some form of 'final sync' option that can be performed.
Though even with this, I would agree with daphnissov that save+quit is the sensible thing to do to ensure currency.
From what I have read, it seems most have success with NOT initially selecting 'Perform Final Sync' option but instead to run the P2V then after this has completed to use the manual synchronize option.
Documentation may give further insight:
https://www.vmware.com/pdf/convsa_61_guide.pdf (can't find 6.2 guide -_-)