It cant be opened in illustrator again? Does it give an error or anything? That actually sounds like a bigger bug than the layers thing. As that is just we dont support their fudge for layers, whereas the not opening breaks the "we write standard svg that should open anywhere" philosophy. May just be AI has rubbish SVG import and cant cope with non svg namespace tags or something in which case its not our issue, but thats something we need to resolve.