@jonathan can provide more detail about this, but here's what's going on here:
When you export, the document name, the JS filename, folder name, etc is all embedded within the generated JS file, which in turn instructs the browser where to look for all the assets required to load your document. This might have changed slightly in the last version, but it's not something we expect users to need to rely on.
There's a line that specifically specifies the name of the JS file, which you can find by searching for
In your broken version within the folder
ERROR changed gnerated script ref, that line was:
d = null != b ? b.indexOf("index_hype_generated_script.js")
If you change it to:
d = null != b ? b.indexOf("ch1index_hype_generated_script.js")
I don't recommend changing this variable as part of your workflow, because it may change in the future. Can you explain a bit more about your setup and tell me about the duplicated resources in your project? Loading the HYPE runtime multiple times should not cause performance issues but I would like to know if you have seen that.