Help!  Pdf losing all non-visible layers

Pdf losing all non-visible layers when saving for first time in Illustrator 2014 (Creative Cloud). The next time I try to open the document it was flat and the only remaining information was (from the visible layers) was locked into a clipping mask. It is like the document was overwrited with a print(flat) pdf. The document also suddenly became 11 pages long (with 10 empty pages).
Anyone knows how/if I can get the information back?

But the editing capabilities box was checked so that probebly wasn't the thing.
Yes I have definitly learned that by now...

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