thanks for sharing your concern.
you have pericoronitis
in relation to your third molar,
this flap which is causing discomfort to you is actually a part of gingiva
covering the tooth.
now when tooth has erupted, it acts like a pocket an accumulates food particles, derbies and bacteria causing infection .
it is better to get it removed surgically because frequent infections are caused in this leading to abscess
and other space infections too.
due to its location accessibility with brush becomes difficult which further adds to infection .
i would suggest , get it excised surgically. it is very minor procedur.
if required an antibiotic and analgesic
can be given.
hope this helps