Just the other day I was playing my flute and I noticed that inside the headjoint smelt pretty bad. Is there any way to remedy this? Can I clean the flute with some antibiotic, like rubbing alcohol, say? Its not a polymer one by the way, its blackwood.
Basic answer is “yes” - isopropyl alcohol or methylated or surgical spirits will not harm the flute (use a spirit soaked cloth on a cleaning rod or piece of dowel), though they may dull any exterior surface patina and you may want to oil afterwards. If you have a fully lined head, you can even push the stopper cork out (so long as you are happy about repositioning it) and polish the metal lining tube with a “silver cloth” or some such. If your headjoint is unlined you will of course need to oil it after any cleaning process. Remember to clean the embouchure hole very carefully - just with a twist of cloth - and to oil its walls afterwards.
As a variation on isopropyl alcohol, it also can be found with wintergreen added to it, commonly sold as rubbing alcohol.
It works nicely on metal flutes, but I’ve never used it on wood flutes.