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yes, the recording sample-rate is always the one jack is running, exactly the one reported by qjackctl and qtractor lower right window corner.

you should be ok with 48k during production and mastering.

only when final, mastered and ready for publishing, you should convert offline to 44k1 to the highest quality possible; you can use eg. sox or sndfile-resample (from libsamplerate-progs).

hth.
cheers