HI
I had the same issue as 1........bugged me for ages
the following worked for me.
open tools/Book Cleaner and in the window that opens, at the bottom load into input file:before formatting 1.bcf and into input file:after formatting 2.bcf , then save making sure you have 'whole' ticked on the loaded book section first, close Book Cleaner.
Then go into settings and make sure the language is set to German. This should now work when you next load a book, allowing all emdashes and 'oe' to show correctly.
as for 2: I always save my book as a Book Designer file first then as an lrf. That way if you ever wish to change formats you can load the Book Designer version and save again as another type of file.
Can't help on 3, but Im sure someone else will be along soon who can