VST to load samples and export MIDI with modulations..? – Effects Forum

Don’t know about plugins, but the DAW itself should be able to export MIDI files (*.mid) from MIDI tracks.

So you should be able to load that flute sample on any VST sampler, record the performance on a MIDI track, then export a .mid file which will include the pitch-bend message, velocity, and any affected MIDI CC.

Every DAW likely has a different way to export the file with the correct data (e.g. tempo/time signature…), so you should probably look into the procedure for your DAW specifically.