The error was happening when KoboTouchExtended driver was doing the work to transform the epub to a kepub. There was probably an error in the epub. An epub-to-epub conversion will frequently fix these errors. And a conversion to kepub, is actually a conversion to epub followed by adding the kepub specific things. That step is identical to what the KoboTouchExtended driver does. As that step didn't fail, it means the epub-to-epub part of the conversion fixed whatever was wrong with the epub. If you still have the original epub, you could open it in the editor and run the error check to see what it reports.
And for the record, the conversion from kepub is basically, remove the spans and then do a conversion to epub. So, you have actually done two epub-to-epub conversions.
The way the drivers work is to look send the format that is at highest in the list of supported formats for the device. For Kobo ereaders, this defaults to kepub first and then epub. That means if you send a book, if you have a kepub in the library, it will be sent. If not, then the epub will be sent. If no supported formats are found, the book will be converted to the first format in the supported list for which you have a conversion output plugin. That means kepub if you have the Kepub Output plugin installed, or epub if you don't.
The KoboTouchExtended driver works like this. It will send a kepub if one exists. Otherwise it sends the epub. But, during the send it transforms the epub to kepub and then sends that over. As far as calibre is concerned, the epub is sent, but, the result on the device is a kepub. Some of the other drivers make changes, but, I think the KoboTouchExtended driver is the one that makes the most changes.
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