Ipad opening old versions even though deleted - can't view new versions!

Question

I am designing and creating iBooks and need to show them to my editor to before they are finished - I export them, upload to drop box and she downloads them onto her iPad 3 Version 6.0.
When I make the necessary changes, i duplicate the file, rename it, and re upload to dropbox. ie 'Joe Blogs 2', that way I have many versions to refer back to if necessary, and i label each one on the cover to save confusion.
Since the new update for iBooks Author we have had some pretty big problems, I have edited, exported and uploaded the books as usual, my Editor has downloaded them onto her ipad, but every time we tap on the new title to open the book 'Joe Blogs 2' it opens an old version 'Joe Blogs 1', even if the old one is deleted from the ipad, also, even if we upload a completely different book it still opens 'Joe Blogs 1' I have changed the titles, and file names and it has made no difference.  we are both using iBook latest update.
NOTE: All books were created from an original template created in iBooks Author version 1, from the 'Basic' template. I have been using this template because I don't know how to recreate it - the are no chapters it starts with 1 page then has sections so that it ends up with a table of contents which looks like this, which means that the 'chapter' (section) title can be tapped and go straight to the section, which is something I would lose if I started the books from scratch (which I obviously don't want to do)

Answer 1

Thank you for replying, and for the tips on templates, that makes a lot of sense - i have now created a template from the original book, and saved it as a template (I cannot make the template from scratch as I do not know how, as I explained, to make a contens page that functions like the one in the picture)
Unfortunately, this has not solved the other problem
Just to check we are on the same page (no pun intended) what I have been doing is this;
• To start a new book: opening 'contents page', a template i have created (and saved as a template, so I get it from the welcome screen on IBA 2, as opposed to opening an existing file and duplicating it.) use that template to create a new IBA file, ie 'Maslen and Mehra 1' which I save, export as 'version 1' when prompted on IBA v2. then I add this to drop box.
after my editor has downloaded and seen it, I make changes, then duplicate and save as ''Maslen and Mehra 2' to show to her again. then I make make changes, duplicate, save, make changes, duplicate, save... up until 'Maslen and Mehra Final Proof (9)'  
since the new IBA update every time she tries to open a new file, the last one I sent her before the update opens (which is really old now as we have made a lot of changes, on our current book we are on version11 but version 3 opens!. Thinking that my template might be the problem I did the following:
• started from scratch: chose an bulit-in IBA template, put a 'A' on the cover, saved it as 'A', exported it, added it to drop box. my editor downloaded and opened it fine.
• changed the 'A' to a 'B' on the front cover (did not duplicate the file)  exported it, I changed it to 'version 2' when prompted, saved the .Ibooks file as 'B' and uploaded it to drop box. My editor dowloaded it fine, and it appears in the library but When my editor opens it 'A' opens instead. 
• Started again (with a completely different built in IBA template) repeated the process, new book 'A' again worked fine, but this did not change to 'version 2'. same problem. new book 'B' opened as new book 'A' again.
• Started again (again with a completely different built in IBA template) this time duplicated 'A', named it 'C', saved, exported 'C' and 'A' still opened even though 'A' is a different file!
• tried changing the meta-data file title, repeated the process, made no difference.
• tried different drop box account, didn't make a difference
• she tried restoring her ipad, still made no difference
• my editor cannot view IBA files (only .ibooks) so we cannot get around it that way...
so my current issues:
• My editor and I need to find a way we I can create a book, send her a copy and make changes, and send her a new copy, whether by duplicating it or even by re-exporting the original document (and saving a copy as a spare) - but neither currently work - why is this so difficult? this was not a problem before the update, she could have multiple books with similar filenames, all orginating from the same file. (which I now know is not the correct way, but even using templates has not made a difference)
• regarding templates: have I missed somewhere that you can make a template from scratch? I thought the closest you could get was to choose an existing template, delete everything then 'add section/chapter' if I go to 'New' in ibooks author then it still just takes me to the template page so I have no choice but to choose one of the IBA templates or one of the ones I have created myself, given the choice I would always rather start from scratch and a blank page anyway! :-)
Thankyou again