When plog-import.php loads, it deletes all directories without files, even if it has a sub-directory.
example: I put pictures in "plog-content/uploads/dir1/dir2/" go to import and "plog-content/uploads/dir1/" is erased because it has no files, even though it has a sub-directory, and that sub-directory has files.
I thinkthis post may be related, but I'm not sure.
For a quick fix, I commented out lines 220 - 225 in "plog-admin/plog-import.php", which removes the cleanup completely.
This should be fixed in the current SVN code (post-RC1 release) and is a duplicate to ticket #237. Can you download and upgrade to the current code and test to see if it works for you?