I prefer to keep the original Native format (could be kept outside Calibre.
I came from the old Analog audio days, where every copy layer (there is a reason, they call them Master copies) results in some loss.
IMHO The same is true with conversions. You end up doing a conversion of a conversion. Each format has it's benefits and drawbacks.
So I try and make all conversions fro the master copy.
YMMV
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