Since I have a fcgi environment I had to modify several .htaccess files. Will these changes be overwritten when I run a composer update down the road? If so, what do I do to protect those changes so the site doesn't crash on an update?
I am interesting in it too, so I ask it in the issue tracker: https://github.com/magento/magento2/issues/2498
I'm interested too.
Updating with web setup wizard overwrites .htaccess as well.