YES is the short answer, you have to open the original itmsp file - iTunes Producer and follow the delivery process.
Remember that it will be considered a version of the original and will either ask for or assign a version number.. in your case it seems to be 1.1.
The original assets, Cover, screenshots, catagories etc are usually all retained - but I am sure when I did delivered a new version, having added the newiBooks file - it too out the cover and screenshots.
As you will need to re-deliver what is to the review team a version - you will also need to add why its a version i.e. Update to metadata, correct spelling.
If you need to re-insert the screen shots and cover and if you did not have a cover which is 1400px across the width - you need to re-size it. Ditto for screenshots which are 2048 x 1536 @264 PPI although I used a resolution of 144 and it was accepted.
Your original book remains in the store as is, your "update" will wait for a review before being accepted, when it is, it will replace the book in the store.
In iTunes Connect, the book will appear with an Orange dot and "In Review" it can take 3 - 10 days for the review team to deal with - when they do and accept you get the usual email notification.
I suggest you go through your book and check for anything you missed and take the opportunity to correct or fine tune anything you see that may improve your book.
I've updated my itmsp file and attempted to submit it, but I'm getting an
ERROR ITMS-4172: "version_whats_new text cannot be supplied for an unversioned publication." at Book (MZItmspBookPackage)
There doesn't seem to be a place I can provide a version # in iTunes Producer.
If I leave the What's New in Version box unfilled, the submission appears to go through.
I had the same problem submitting a 'new' version of an older unversioned (version null) book. I exported from iBooks Author with the share menu item. It has you choose book or sample. With book you can specify a version. I stsrted with v1.0. When I updated the itmsp file I choose the new v1.0 .ibooks file under assets. I added some what's new text and got the same error message that you did. I took out the what's new text, re-delivered which worked ok except for a warning that what's new text was required before it would appear on the bookstore. Hmmm. I waited awhile and found reference to the v1.0 book on iTunes connect. I then added what's new text to the itmsp file and re-delivered, went ok with no warning. After the review period the new version was online...
So after contacting Apple support, changing the category or metadata apparently has to go through them:
Thank you for contacting iBookstore Publisher Support.
Upon review, I understand you would like to update your book's metadata. Once a title had been successfully uploaded to us and is live in the iBookstore, certain changes to the metadata (i.e. book title, subtitle, author name, category and/or book description) need to be requested and made through us.
I have received your request to update your book's category, and am escalating this to our Book Review Team. You can expect to receive a response within 3 business days.
If you need assistance in the interim, please contact us again by responding to this email.
Less than 2 hours later, I got:
Great news! Your request below was approved, and the updates to your book will be reflected in the iBookstore within 24 hours.
If you have any further questions please don't hesitate to contact us again.
And the new primary category was reflected on the iTunes store shortly after.