An ePub must be in UTF-8. Some readers are more forgiving and don't follow the spec closely, but ADE may well complain. Frankly, I think the best thing is for you to make a short ePub and upload it so we can see what's going on.
No, copy-protecting the ODT will not copy-protect the ePub and will probably just cause more problems. Forget about copy-protection unless you have $$$$$$ to spend on a content server for a DRM-scheme that's already cracked.
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