It does sound like an outer ear canal problem, from the squelching symptom. I suppose your ENT had a look and excluded wax (cerumen) and foreign body in the ear canal. You should have any wax treated and use ear plugs when swimming. If it is an outer ear problem, it would have little or no impact on your fitness to fly.
More of a problem for flying would be middle ear problems which would affect you more during ascent / descent, and would need treatment with antibiotics or even grommet drainage tubes.
In either case make sure you have had a proper and thorough going over from an ENT surgeon please, not just your family physician.
Regards,
The plumber