hi and welcome to HCM,
The CPAP machine is a non surgical and good alternative treatment to obstuctive sleep apnea
But it shows some of the disadvantages like dry nose , sore throat
, sometimes running nose , nasal congestion
As you have mentioned swelling of the tonsills and throat mucosa may be a side effect of the use of machine.
you may be able to limit or stop some of the disadvantages of the machine ,be sure you fit the mask or the nasal prongs properly to avoid any leak
consult your doctor who will adjust the machine properly to eliminate the problems.
i hope this helps ,