Recently, I had a sim session and handled a windshear exercise immediately after T/O. Airspeed went way above S momentarily while I was maintaining FD.
In my opinion, FD guidance will adjust accordingly to prevent such speed excursion, so I shouldn't retract the slats/flaps and stick to the written procedure
Following the FD "in windshear" can mean a number of things. Was the Windshear encounter determined by the Windshear Warning (in which case FD gives appropriate guidance)? Or "pilot assessed", when you just get normal SRS commands?
You then have the Aa issue, where the FD might change to CLB, but if still in windshear, it might be inappropriate to follow it.
Bottom line though is if you have not yet clearly communicated between the crew that you are clear of the shear, and adopted an acceleration profile, then you maintain config from my training.