You do not lose books marks if you remove the SD or memory stick card. I always remove mine with the reader off and all the bookmarks are still there when I insert the card again at a later date.
Ive only had my reader a week and this was one of the first things I testes since that 512 memory just isn't enough for me. To be fair I am using a memory stick pro duo and I have not tested this with the SD card. But I doubt it would be any different.
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