May I point you to http://bugzilla.lyx.org/show_bug.cgi?id=3561 again?
This is a critical bug for quite some time in bugzilla without a clear explanation what the problem is. I added this now as a comment. It has not much to do with the source view, but with encoding changes in general, also during TeX export. You basically cannot export documents with paragraphs starting in encoding A and finishing in encoding B. I think we should really fix that before RC2 (I hope it's not too late).
Stefan
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