Catherine Ilioni is ultimately only known today as a result of her tombstone having the earliest known image of the Virgin Mary in China. The community she was a part of was one of traders, and not really well integrated into the larger society in Yangzhou as a whole, and not one about which too much was written at the time (or at least among those sources which have survived to the present).
What you're seeing with "thriving community" is in part a reference to Franciscan missionaries and affiliated trading families. The Franciscans sent missions to court the Yuan and spread Christianity in China. It was short lived and by the time the Ming took power, the Franciscans were essentially sent away. However before that point, they were quite active throughout China and Asia as a whole.
As with a great deal of other instances of missionaries in China, their efforts were inextricably tied with trade. With the Friars and Bishops came traders, and Katarina Ilioni was one of their number.
As for what happened to those who didn't die there, it's not clear, but it's unlikely that they would have remained after the regime change, and if they did, it's unlikely that they would have survived. The Ming was quite closed off, as they are well known for being. Later (edit: Franciscan) attempts to send foreign missions to the Ming did not end well for the missionaries.
Expanding on this, were there any similar enclaves of Europeans living in China around this time?