If you use calibre, it supports resending a book to the device without losing the reading status or annotations. But, this only works if the internal structure of the book hasn't been changed. If you are changing styles, fixing spelling or grammar, it will work. But, if you change the ToC or the internal file structure of the book, there can be problems. The book will probably open, but navigation probably won't. And annotations probably won't be linked properly.
If the book format is ePub, and you are not using calibre, replacing the file can work. The book will be added as new book, but, the annotations are stored in two places. The main copy in database will be removed. But, there is a copy created by the RMSDK. When you open the book, this is read and loaded into the database. There is some information lost, but, assuming the structure of the book hasn't changed, it should work.
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