Presumably the 're-upload all pages' bit can be automated. As far the reset, the trade-off depends on how often you're updating content versus the amount of traffic coming to your site; in many cases, a tiny saving on frequently-occurring page delivery is well worth a big delay on one-off page generation.

rsync will easily handle a few lines changed in a large number of files.

Or you could just, y'know, run the static site generator on the server. What Linux doesn't have Python installed?

>and much slower for you when you make a minor header/footer mod locally, and then you need to re-upload all pages that have a header

You should automate that with Grunt or Gulp. Static .html pages is best practise these days instead of dynamic templating.