If a book file path changes as a result of the folder restructure (which I assume it would), then the progress will be lost. The book progress is associated with a specific book and changing a book file path effectively results in a new book.
I understand that you are using eLibrary Manager Basic, but just so you know, in the full version, book position for the last 20 books opened (configurable, so it can be set higher) is saved based on book title and author(s). In that case, if a book file path changes, then as long as the title and authors remain the same, the first time the new book is opened in the reader, it would open at the last reading position (and therefore restore the progress).
So I guess the bottom line is that, in the basic version, there is no way to easily carry over book position and progress if the book file is moved to a new folder in the device file system. In the full version, you could carry over the last 20 opened book positions (and progress) as long as each of those books is opened in the reader which would restore the last position.