Stop all running Biztalk services, load up SQL Management Studio, on the BiztalkDTADb database run the following script. Note that this script does not archive data.

declare @dtLastBackup datetime
set @dtLastBackup = GetUTCDate()
exec dtasp_PurgeTrackingDatabase 1, 0, 1, @dtLastBackup

After this has completed you can shrink the database files.