I could be wrong but I don't think the cotton tip would reach the ear drum, would it? Even so, it sounds like he may have done some damage.
Our first experience with perforated ear drums (only about 6 weeks ago) is very similar to Isoabella - 4yo went to bed vaguely unwell, had had a dose of panadol but couldn't really explain where he felt unwell. About 2am he was beside himself with ear pain - it was just awful it watch

I had literally got off the phone from the doctors surgery at 8am when he said "my ear feels wet" - it was almost pouring with clear fluid - and the pain almost immediately stopped!
The GP couldn't say for sure whether it was a perforated ear drum as he couldn't see well enough with his instrument due to the amount of fluid. We happened to have a ENT appt the next day (!) who confirmed that the grommet put in 6 months earlier had already moved and it was indeed a perforation.
Now, only a few days before Christmas, my husband and I thought out 9 mo was only a little grizzly and his ear smelt (!). No temperature but we did pop him into the GP who confirmed a perforated ear drum. Later in the afternoon, a little bit of thickish fluid began to discharge. We actually suspect he has another ear infection and he is off to the GP again tomorrow morning

Perforated ear drum sounds terrible, and the pain must be awful, however since these two occurances with my boys I have spoken to quite afew other parents who have had expereince with perforated ear dum. My two main questions for the doctor tomorrow are: How do we prevent it (they don't go swimming), and I am too concerned about the risk of hearing loss if it continues - perhaps our little one is a candidate for grommets also?