I'm sorry to hear about your Wax Moth infestation! The gauges and scars left by the larvae and cocoons should not impact future colonies that inhabit your TBH. Many people are intentionally scarring or roughing up the inside of their hive cavities to encourage the bees to lay down more propolis. Propolis has antimicrobial and antibacterial properties, so this may help increase hive health. If you are worried about surviving cocoons on the top bars or anywhere else, they can simply go into the freezer to kill off any stubborn survivors before being put back in the hive.
In general, Wax Moths do not become a problem for hives unless they are already very weak or have low numbers. Honeybees are great at clearing out unwanted larvae and cocoons, so the silver lining here is that the weak genetics of your colony are not being passed on, and you can get stronger bees next year!
I hope this helps!