A recent post in this Forum asked about Rubbing Alcohol, etc for disinfecting liners. As I am not allowed to respond to posts in this forum, I am posting a new thread.
First, Spray with with either an antifungal spray or good ol Lysol and let it dry.
Second, go to a bootfitter and have them heat mold the liner (in the process killing any bad stuff still there, same as cooking does for food), as long as their process goes above 140F.
PS, while you're there, check out some custom corks, I love mine.