I find this kind of strange since I have imported tens of thousands of files into Objectify without a problem. But I was just importing a few thousand files (using --recursive on some directories) and when I ran a verify_file there were two different errors on a few files. See Bugs #2427250 and #2427286.
To be on the safe side until I can find what these problems are, I would ask that you keep a backup of some sort (compress_sparse or keep .dif files). Also after using import_file, always use verify_file to make sure the files were imported correctly.
And if you have any sort of error please report it.