(edited for an early morning math error, as I was doing the math in error on 14T not 16T)
A 52/36 technically exceeds meets the 16T capacity of a Dura Ace 9000 series front der. As such, you might expect to have some rubbing in the small ring, especially if you choose to leave the der positioned slightly higher for the 53/39 crank. Ignoring the capacity issue, I'm sure shifting would not be sufficiently degraded if you left the der unadjusted for this to be a temporary solution. If it were my bike, I would be adjusting the der and cable as part of the swap over, as I see it as only a few more minutes work to ensure optimal shifting while riding.