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Currently vCenter Protect does not patch VMware Tools. For now you could look into creating a custom patch or custom action within Protect to push out VMware Tools. I'd suggest looking up these options in Protect's Help section if you're new to using them.
Otherwise, submit a request here to have VMware Tools added as a supported product: http://shavlik.featureidea.com
I know this is an old thread, but this can now be completed. Out-of-dated VMware Tools will now show as missing in a security patch scan. Just right click and deploy, and the upgrade works great. And even better, it doesn't mess with Agent statues if you are patching your VDI's.