In most case, you would replace
with
however it appear the link to the CSS file is not found in the template Individual.htm. Ron designed the report templates, maybe he help better than me.
It is there following any Timeline JSON data at around line 91
However all links internal to the report are relative, so changing the folder level will effect all links. I suggest you try adding an HTML <base href="URL" /> tag to the individual.htm template to compensate for this, where URL is the URL of your report output folder.