Which Sony eReader with a touchscreen did you try? What kind of screen protector did you apply? The PRS-600 style touchscreen is different than the PRS-350/650 style. The latter uses IR transmitters/receivers in the bezel, like the Kobo, Nook STR, and new Kindle Touch devices. I'm not really sure what technology the PRS-600 used (not sure if it was resistive or capacitive), but I suppose that could maybe be affected by a screen protector. On the IR models, as long as the screen protector is thin and applied correctly it should not interfere with the IR grid projected on top of the display.
Also, eInk isn't that fragile. You're unlikely to damage it through regular touching, or there'd be tons of posts of broken Sonys, Kobos, and Nooks. IMHO, if the developers wanted a screen protector over the eink screen they would've put one there and so I don't use a screen protector on any of my devices (not on my phone, not on my Nook STR, and not on any of my tablets).
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