I just noticed a new feature "Download All" in the library. First I thought it is just either to get all the library (4000 books in my case) or nothing. When I tried it this way, I had to re-install Logos to my iPad because I run out of space. (I have 32 GB iPad2).
Then I tried to use filters and to my amazement it downloaded only those books listed by the filter! Great feature. Thank you Logos.