If everything worked correctly, you should have exactly 2 files now, a small metadata file and a large data file. The data file should be about the size of the storage folder, and the metadata file should be about 1/200,000 the size of the data file.
If you have 4MB files remaining, that means that somewhere along the line some data got left behind. You can delete it now. It may have just not been cleaned up correctly, it doesn't necessarily mean the data was left behind or lost.