Hi Mike,

If I were going to try etching each side independantly (which I wouldn't because it isn't even close to worth the effort), I would try to save the white adhesive film to put back on the side that was already etched. Even if you take the time to mark over all of the traces with a marker (or an etch resist pen), the etchant will eat away the copper underneath the etchant barrier by undercutting. This also happens when you etch the board to product the features, and is why trace cross sections are trapezoidal instead of rectangular. This is also the reason that heaters, aeration agitators, and recirculation pumps allow you to etch smaller scale copper features. Anything that reduces the total etching time will reduce this undercutting effect.

Seriously, what you are suggesting is a whole lot more effort than putting a fiducial datum on each of your transparencies.

Good luck,
Joe