If a tree containing a non-annexed file (checked directly into git) is exported, and then an import is done from the remote, the new tree will have that file annexed, and so merging it converts to annexed (there is no merge conflict).

If the user is using annex.largefiles to configure or list the non-annexed files, they'll be ok, but otherwise they'll be in for some pain.

The importer could check for each file, if there's a corresponding file in the branch it's generating the import for, if that file is annexed. This corresponds to how git-annex add (and the smudge filter) handles these files. But this might be slow when importing a large tree of files.