FFF stores the chapter URL in a
<meta> tag in the header of each chapter file. When it doesn't match, FFF assumes it needs to be replaced.
You could try removing the
<meta name="chapterurl" ... > tags from the epub before updating with the new site--if you are
very confident that the chapters line up the same.
But it would be a lot safer to download from the new site as a different book. You could use a storyUrl personal.ini section to set first_chapter:X for the new URL to force FFF to always act as if you'd entered the URL with [X-] after it.
first_chapter is an undocumented feature, but we're already talking about unsupported sites, so why not.
Setting
continue_on_chapter_error:true records failed chapters while continuing on. Error chapters will be replaced, if possible, on Update. Note that FFF will continue to try every chapter--so if starts failing at chapter 5 of 500, you may be waiting through failed 495 chapter attempts.
Setting a
slow_down_sleep_time of a few seconds for the site may well help.
I've
explained before how you can break up the download of long stories using the chapter range feature on the story URL.
(And please don't call me Jimmy.)