When I've soaked bottles to get the labels off, I haven't used anything other than water. Just some good hot water to fill up whatever you put them in (I use a cooler), then let them sit for a day or two. Most of the time the labels come off pretty easily. Then just a quick little scrub with soapy water (I've used dish soap) to get the last bit of residue off and they are ready to go.
I don't think there is any reason to use other chemicals. There have only been a couple breweries that have had labels that were tough to get off the bottles (damn you Breckenridge!!!).
I can't help you with deciding if those etched bottles are still safe to use, but hopefully you won't have that problem in the future.
On deck - a few single hopped pale ales - Cascade, Calypso, and Legacy
Primary/Secondary - Chris' Tall Ale (a Belgian golden ale); The Land of Pils and Honey, an imperial Saison with Clover Honey; Northern Brewer's Oud Bruin de Table / nada
Bottled - a sour mashed Berliner Weisse; Cascade Pale Ale; Hop Wine - an Imperial India Pilsner Ale; Guajillo Ancho Brown Ale; Back To School Porter, an Imperial Robust Porter with vanilla beans added