Take care not to duplicate *.iba files. If you do, the *.ibooks files created with them will all have the same internal IDs. These IDs are neither visible nor changable. This causes identity problems in the iBooks app. Opening book A might actually result in book B opening because they have the same ID. Always create *.iBA files from a template.
So your tactic is effective but dangerous. This problem is easily solved by using File > Save as template ... to create another copy of your *.iba file. It's an extra step but it insures that you will not accidentally create two or more *.ibooks files with the same internal ID.
I discovered this the hard way when I taught a private iTunes U course containing six *.ibooks files created with duplicated *.iba files. The books were issued sequentially so by the third book, we were all totally confused as to what was happening and why. Once I got the answer (from Apple), I created new templates for each book and exported new *.ibooks files. That solved the problem.