That's where things get tricky, and in an attempt to avoid confusing everybody even more, I left that detail out of my explanation. The issue here is that XenForo only works on the template level. It doesn't have the ability to break down a template and find out which specific blocks of CSS have changed or which haven't. It only knows if the entire template has been modified or not.
So in your footer.css example, even if you just modify one line of CSS, XenForo would consider that template modified and it would
not update if you updated the parent. It would remain completely intact because of that one modification.
So, in your first hypothetical scenario in which all 20 templates are modified, when you install/update the parent Flexile template,
not a single template would actually be updated in the child style, because they had all been modified, and the modified templates in the child style take precedence over the templates in the parent style.
So, in effect, updating the parent Flexile style in that situation would do nothing. This is where you can theoretically run into problems if you've customized Flexile heavily. Because any templates that you've modified in the child style will have priority over their parent counterparts and thus will not be updated when you overwrite the parent Flexile style, it's possible (and probably even likely) that you won't get some of the changes or updates that I've made in the new version. This could in theory lead to hard-to-diagnose style issues if there are missing template hooks, inconsistencies, etc.
There's really no way around this other than to put your
all your CSS edits/overrides in EXTRA.css and leave the rest of the CSS templates untouched, so that the child style will inherit them from the parent style and thus will inherit any updates too.

However, this doesn't help for HTML templates. In those cases if something goes awry you may just have to revert the template and start clean, or manually transfer the updates yourself to your customized versions (this is what I have to do each time I update Flexile or Flexile Dark - it's about an hour long process, although it depends on how many templates differ between each version of XenForo).
As I said in my brief post about this on page 10 of this thread, "such is the life of customizing themes."
