For those type of books, I make a decision about whether to leave it on the last page, or finish the book and accept that I have to find the position later. The decision really comes down to whether I think the book will be actually be updated, and whether I think I will read it if it does get updated. If it is a good book, and appears to be being updated, I stop on the last page. I'll probably remove it from the home page on the device, but, it will open to the correct place when it is updated. Otherwise, I just finish it and accept that I have lost the location.
At the moment, there is no way to restore the bookmarks. I may look at that when I get around to storing annotations as calibre annotations. But, don't hold your breath for either of those.
If you were reading epubs, the bookmarks would be reloaded from the RMSDK annotations file when you open the book. But, that isn't used for kepubs or other formats.
For the foreseeable future, the simplest way is to stop on the last page, and either dismiss the book from the home page, or set it to read using the metadata update function.
Of course, for an FFF produced book, creating the correct location isn't that hard. The start of the chapter would look like:
kepub:
Code:
OEBPS/file0002.xhtml#kobo.1.1
epub:
Code:
OEBPS/file0002.xhtml#point(/1/4/2/1:0)
And it would probably work without the fragment. You could point to the new chapter when it is updated and update the location after sending to the book. There might even be a way to automate that with either FFF or Action Chains.