If I place custom files in WordPress root, will they be deleted?

Taken from this link there are several other options for adding your own CSS, if you don’t want to put it in the theme:

  1. Use Theme Options and paste in CSS
  2. Use a plugin to insert CSS/JS. You could also write your own plugin to ‘host’ the CSS file neatly in wp-content/plugins/ somewhere.
  3. Use a child theme, which will maintain your changes if your theme changes.

More info on each of these is in the link