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.
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