Update all the references in theme.less to point to bootstrap sub-directory. Ensure that your variables.less is referenced from the parent and not the bootstrap directory like so:
...
// CSS Reset
@import "bootstrap/reset.less";
// Core variables and mixins
@import "variables.less"; // Modify this for custom colors, font-sizes, etc
@import "bootstrap/mixins.less";
// Grid system and page structure
@import "bootstrap/scaffolding.less";
@import "bootstrap/grid.less";
@import "bootstrap/layouts.less";
Link to theme.less instead of bootstrap.less in your HTML pages.
Whenever a new version comes out, your changes should be safe. You should also do a diff between your custom bootstrap files whenever a new version comes out. Variables and imports may change.