Fingerprints are stored in a large number of small XML files in a certain folder (by default, called fingerprints). This makes it really slow to move around data by file copying, as the OS will search the files one-by-one in order to copy, and they tend to be very scattered on the physical disk space. Further this is very space-inneficient, due to a lot of wasted disk space due to file allocation tables which typically allocates multiples of 4 kb blocks for files. Further, space is wasted in some directory allocation tables too.
Please, put the fingerprints together in a single file, or at least group them in a smaller number of files.