Jonathan, I know what you mean. The idea is that zero may be taken as false (no 
id 
provided). However, my test now seems to behave (12.1.14)

The line in Jmol.js that does the trick says
   nameSuffix == undefined && (nameSuffix = appletCount);

but I really don't understand how this code works.

What exact code are you using to destroy and recreate the applet?
I have tried 
function destroy() {
  document.getElementById("cont").innerHTML="";
}
function create() {
  jmolSetDocument(0)
  document.getElementById("cont").innerHTML = jmolApplet([width,height], 
scriptStr, n)
}

where "cont" is a div containing the applet




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