The position, length and form of a tone hole will determine the intonation and sound character of the particular note. The shape of it can be rather complicated. In addition to the pitch the tone-hole is associated, it can also have a significant influence on the surrounding notes. Finally, it is very important, that it is perfectly airtight when closed.
This makes the quality of the tone hole very important. Any damage will automatically have a negative influence. Damages can even be found on brand new instruments and ought to be fixed.
This is the case when the intonation or sound of a particular note is problematic. The L&P voicing procedure will take care of these problems. It sounds much more dangerous than it is, whatever changes we make, can always be reversed.