Daily maintenance

Swab out your flute every time you play.  You can use a cleaning rod and soft cloth or other swabs designed to clean out your flute. 

About so-called pad savers:  Do not use these to swab out your flute and then store the flute with the damp pad saver inside.  Instead of making your pads last longer it will actually cause them to wear out more quickly.  If you want to use a pad saver, swab out your flute with a cleaning rod and soft cloth first and then insert the pad saver for storage. 

If you get moisture in your pads when you play, use lens tissue or perming roller papers to gently blot the moisture out of the pad.  Do not use a dollar bill.  It will get the pad dirty.  Do not pull the paper out while blotting.  You will fray the skin on the pad and make them wear out too soon. 

Periodic maintenance

Take your flute to a reputable repair shop every year or year and a half for a regular oil and adjustment.  Like a car, the lubricating oil on the mechanism gets dirty and needs to be cleaned out and replaced to prevent undue wear on the mechanism.  If you do not damage the pads, they should not need to be replaced very often.  When they do need replacing, it is usually one at a time. 

Unless you have had some instruction in flute maintenance, it is unadvisable to do this yourself.  Getting the mechanism and pads to all work together and seal the tone holes properly is something best left to professionals. 

Getting an overhaul is a really drastic measure to take to fix a flute.  It is not recommended unless the instrument is in really terrible shape.  It is much better for the instrument to change pads as needed and replace corks that have fallen out.  The instrument will be more stable than if you change everything at once. 

If you take your flute in for repairs and problems are not fixed properly, insist that the repair person fix the problem properly.  In future look for another repair person or shop.  There are a lot of music stores and repair people who believe that the customer will not know the difference and so do substandard work.  Most people will do a good job, but be alert to the quality of work.  If you get an overhaul and your flute plays worse than when it went in the shop, it is not you!  The shop did not seat the new pads properly.