First, you don't normally need to reflash, there's just been the one official update from Sony, so it's not a frequent issue.
Most of the recent issues about reflashing have been where people have wanted to use that update to 'downgrade' from the European versions in order to be able to reflash with tweaked firmware, which itself requires an SD card, not a Windows PC...
Calibre doesn't have anything to do with reflashing, it's for transferring books.
Just to clarify, Calibre & Sony work together happily enough as long as you don't try & use both at the same time, as they both need to write to the same 'index' file on the reader. If you only use one per 'connected session', you'd have no problems.
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