Hi,
The comment that all RealTracks and Drums that have previously been released are included in the current full packages is correct. So you should be able to replace your RealTracks and Drums folders with the shipped ones, unless you have added files to those folders yourself. The drives do not include Xtra styles on them, so if you have any Xtra styles, XPro styles, Loops-with-styles, those need to be installed to the drive - that would add some files to the RealTracks Data folder (mostly style audio demos).
The current Audiophile drive does ship with both .wma and .flacs, since some people want to copy the .wma's to their internal drive. This may change if it seems that people are happy copying the 600GB bb folder to an internal drive (saving 160GB or so by not having the wma's). We plan to add a BiaB feature to delete unneeded wav/wma files, however this is not currently in the program. As noted by a few people it is definitely possible to do with a script, however you have to be very careful because unexpected things can happen and end up deleting files you didn't intend to.