For an existing app, you can't just remove bootstrap and put in something new. As you probably realize by now, everything will just break.
Instead, you need to update individual pages along the way. This process is preferable to removing bootstrap and re-implementing your pages all in one giant pull request since it allows your team to QA iteratively.
For us, we redesigned our app, made it responsive, and also used another library in addition to removing Bootstrap. There was a lot more nuance involved, but for example, I started first by redoing the header and footer, then I moved onto individual pages. You can probably just start by re-implementing common mixins and modules first. Then you can move onto the actual templates and start removing your .rows and .span divs page-by-page.
I wrote about the process in depth here: https://medium.com/anyperk-product-engineering/anyperks-resp...