It should go back to being flat after putting the new transom in.
When you clamp it, a few things to consider.
Use as many clamps as you can. Always start at one end and clamp progressively to the other, and bottom first then the top. This way it helps move air pockets up and out.
Don't place the clamps directly on the transom, especially if you'll be using the Vise-grip style hand clamps. Use boards of 2x6s or 2x8s between the clamps and transom. This distributes the clamping pressure over a wider area, and prevents "dents" being created due to the pressure.
If you have a piece available, on the back outside part of the transom use a piece of plywood 1/2" or thicker between the clamps and transom. This will help flatten the skin as you'll essentially be sandwiching the exterior skin between it and the new transom.
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