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Lower the priority as suggested.
Limit the number of cores (IIRC must be multiples of 2)
Just be aware that many Conversion are AN INTENSE computational and Memory tasks. (Games are Intense Graphics tasks)
Be sure your Computer cooling is in A1 shape. Run smaller batches to give it a cool-down break between batches.
The only advantage of a Bulk convert is fa aster transfer to your K.
Calibre will convert on the fly (It does take the same time as the demand conversion) any book not available in the AZW3 (or Mobi) format
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