How to force the update of a gem with bundler?

First of all, don't do that. If you change your gem, you should be updating its version number. Otherwise, it's just confusing.

If you really want to do this, however, you can apply the giant hammer of removing your gem first.

$ gem uninstall foo
$ bundle update

you can also put the git hashref right in the Gemfile with the :ref option

gem 'foo', :git => 'git://github.com/foobar/foo.git', :branch => '0.9-beta', :ref => '9af382ed'

especially useful if you don't have control over said gem, and keeps bundler from giving you a newer version in case there are breaking changes.