git rebase conflicts?

If I'm rebasing the history on a project, basically squashing all commits to a point, why are there conflicts?

Keep in mind this is a flat history. Basically the history came from SVN and now I'm trying to squash that down to "this was the stable migration from SVN".

So howcome when rebasing it causes a conflict? Some times its files that are missing, or being deleted. Some times I can see it's because an empty directory (at least that makes sense with git).

Any other suggestions? What I really want is there to either be NO conflicts, or simply conflict resolve with the correct (newer) file.