If you never want to send PDF the Kobo, you can remove PDF from the list of formats for the device. This is done in the drivers configuration. Right click on the device button when it is connected and select the configure option. Then find PDF in the list at the top and uncheck it. After you save the change, you will need to restart calibre.
With this in place, if you do try to send a PDF to the Kobo, you will be prompted to convert it first. Answering no at that point will stop the send.
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