Booxstor, it seems to me, that it is true only for sketches, annotations and maybe something more.
I made a test quite recently and it seemed to me that bookmarks (and possibly other data concerning document) are saved somewhere else. Not in *.sketch file in .Onyx folder. (Now, I realised that there is also one common file in .Onyx - the document data could be there ... But it does not solve the main Edmond's problem. The desire to rescue the bookmarks.)
The main problem Edmond has, is that (I think FBreader) wrote (probably) invalid value of current page to database, which is a bug. And none of 3 readers is able recover from this errorneous state, which is 4 bugs (1 - programmers should/could check if the value read from database is in range of document size, 3x1 - each reader should behave decently even if the page value is invalid).
He invested quite a lot of time to make bookmarks and he needs them recover. So, deleting approptiate file (not whole .Onyx folder - it might erase annotation data from other document files) in appropriate .Onyx folder. is not solution for him.
Despite the fact, where the current page possition data is stored, it would be highly desirable to fix at least reading from database bug (make easy check if page number is in range) and also the source of the inconvenience - make page range test in GoTo Page dialog code, so that it returns a valid number if user inserts no value.
It is not much work for programmer. Could be between 10 minutes to hour or two (if it is really difficult).
I rechecked if bookmarks and Last Page Read are stored in .Onyx\*.sketch or .Onyx\thumbs.db files. They do not seem to be, unless I made a mistake.
1) Open document, go to any page except of the first one. Place there bookmark and leave the document.
2) Erase .Onyx\*.sketch and .Onyx\thumbs.db files.
3) Re-open the document. Document does not open on 1st page (but the bookmarked one) and there is the bookmark.
Both, the Last Page Read info and bookmark info and Bookmark info survived deletion of both files, so the info must be stored somewhere else... Probably somewhere on system partition. One probably looses bookmarks if moves the document file. And it is not possible for even quite high above average user to backup his/her valuable work