When QtCreator realizes that file has been changed externally, it asks user if he wants to reload file. And if user agrees, Creator reloads file removing all bookmarks associated with it (In the same way as if user explicitly removed file contents with Ctrl-A, delete).

Since reloaded file will be with high probability close to original one (for example, git checkout changed file) and there is no way to undelete automatically removed bookmarks, I consider current behavior as a bug: Creator should try to retain bookmarks.

Kick-ass solution would be deriving where bookmark should move by running diff, but simply holding bookmarks on lines they were before is enough (for me).

Here is how I solved it for myself:
http://qt.gitorious.org/~igogo/qt-creator/igogos-qt-creator/commit/a493c77c7366c7e6ab5bef4e7f0f12090ffe7f89

The solution is not very elegant, but maybe it'll help you to find right way .