AFAIK calibre will automatically clean up the folders it empties, and you cannot tell it to stop doing so.
It usually isn't a problem, because if you can tether your device to delete the book using calibre, then you can likely tether your device to upload the new books as well.
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On the topic of templates, you say you have a Send-to-Device template but calibre does not use that template when building the filename of a book you send to the tablet?
Can you double-check that the template is set in the device driver for your tablet -- I believe tablets always require the device-specific override.
See the attached screenshot for configuring the device driver.