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You can perform inplace upgrade from AX2012 to AX 2012 R3.
(Scenario: Perform in-place upgrade to AX 2012 R2 or AX 2012 R3 [AX 2012] –
Check for scenario upgrading from AX 2012 or AX 2012 Feature Pack)
Check this Forum topic for further details : https://msdynamics.net/forums/topic/in-place-upgrade-to-ax-2012-r2-or-ax-2012-r3/