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When you disconnect the Kobo ereader from the PC, it looks for changes in the books. Any new books will be processed into the internal database and hence the library. Any books that have been deleted, will have nearly all evidence of them removed from the database. Any changed books will be removed from the database and then processed as a new book.
The behaviour of the last one has changed over time. Early firmware didn't do anything. Current firmware does the above.
For this, what the firmware considers as changed is the file size. That means you could unpack an epub and repack it without any other changes and get a different size. Or open it, change one letter somewhere in the text and repack it and the device will see it as a new book.
Because of this, when you send a book to a Kobo device that is already on the device, the driver will update the files size stored in the database. I chose to do this in the driver because that kept older behaviour, and my impression from discussion here is that how people wanted it to work. And to be honest, it is how I wanted it to work. I frequently edit books I read to fix spelling and layout. As long as I don't fiddle with the internal file structure or the ToC, everything will work OK.
If you make changes to the ToC or the internal file structure, the book can probably still be read, but, there might be problems. One of the things that the processing of the book does is to store the ToC in the database. If you open the ToC when reading the book, the database is used. If it doesn't match the book, selecting an entry will probably take you to the start of the book.
If the file structure changes, again the book can probably be read. But, the ToC won't work and the reading position won't be stored properly. That means it will probably reopen to the start of the book.
None of this has anything to do with the utilities plugin. It's how the device works and how the driver works.
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