It makes the upgrade process easier if you stick to only making changes in their variables.less file[0], or even better creating a copy of it and including that instead in bootstrap.less. Heck, you can even just create your own top-level myproject.less file and copy over the includes you need using bootstrap.less[1] as a template.
[0]: https://github.com/twitter/bootstrap/blob/master/less/variab...
[1]: https://github.com/twitter/bootstrap/blob/master/less/bootst...