Following up because Itch support doesn't give a crap about their clients and won't get back to me.
I removed the original file and created a new one manually which seemed to fix the problem for now.
However, by deleting the original download, it also removed all the exposure (views, plays, downloads) the game had been getting, and as a result the game has dropped from top 10-20 in the HTML multiplayer section to several pages down (about #66) now..