Are you talking about in calibre or when the device does the import? On the device, there isn't anything you can do. You have to fix the broken one, or remove it, to do more.
In calibre, I think this means you are using the KoboTouchExtended driver to send the books as kepubs. If so, there is an option to "Silently ignore failed conversions" in the driver. If you turn that on, if the transformation to kepub fails, the epub will be sent instead.
If that isn't the case, we need to know what the error is. What to do depends on the error. It might be possible to continue, but it might also be a bad idea. Or just not possible.
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