Though the process should be able, and usually does, handle massive updates; it is best to transfer large libraries in smaller increments. The best way to select a subset is to select a reasonable number of songs/tracks within the remote library and then clicking synchronize. SuperSync will warn you (once) you when you are about to synchronize more than a hundred tracks.
If you are deleting an entire hard drive of music, its best to manually do this.. using SuperSync's trash feature will take a long time to notify iTunes that each track should be removed. Close SuperSync, delete the tracks using iTunes, or alternatively, delete them on the hard drive and then delete them in iTunes (to clear the metadata).
Run Rescan after the library synchronization has been completed. Exit and restart SuperSync and do another rescan of the library if you want to be sure things are where they should be. Again, if you use iTunes, the iTunes song track count and SuperSync track count should match. Note, if iTunes supports a file format that SuperSync does not support, these the counts may be off.
Pause server updates or disable the SuperSync server when not needed. The same goes for the iTunes music server.
While transferring large libraries, it is usually best to turn off the SuperSync server updates on the end where the iTunes library is being updated. For example, if you are sending songs from a Macintosh computer to a PC to update the PC's iTunes, turn off the server updates on the PC. To pause server updates, select File>Pause Server Updates.
Playing music while receiving new music on large libraries should be avoided if you hear skips in the music. While it won't hurt anything, it sounds like your computer may be working hard enough, without the added CPU load of decoding and playing music.
Ultimately, the speed at which libraries can synchronized are
constrained by several factors:
1. The speed of the computers involved. This includes:
1a. The amount and speed of the system RAM.
1b. The processor type and speed.
1c. The speed of the disk drives, the type (NTFS or FAT for example)
and fragmentation of the file system, and the amount of free space
(though not the size of the disk)
2. The speed and capacity of the network connecting the two computers.
3. The size of the libraries.
4. The number and sizes of the tracks to be synchronized.
5. The number of tracks in the existing library (which determines the
size of the iTunes meta-data file).
Adding additional tracks to a library with 1,000 tracks already loaded
will be significantly faster than adding tracks to a library that
contains 10,000 tracks. Fundamentally, iTunes is making updates to
its meta-data file for each track added to the iTunes library and as
this file grows in size the time it takes to manipulate it increases.
These factors are only of interest for those among us that have substantial libraries that we are moving around.If your library is smaller few of these factors will be of issue.
Pausing iTunes and Server updates is a good idea. If you aren't using the SuperSync server, disabling it can improve performance.. because SuperSync updates the server as tracks are added--whether or not anyone will ever connect to your machine.
SuperSync has a significant number of status reporting tools and displays. Use them to manage your process. For example, the iTunes status display will tell you if you are making updates to the iTunes library. Also, you can monitor this process by looking at iTunes itself and by sorting by the "Date Added" column. You can sort "down" so the latest adds are at the top.
If SuperSync and iTunes get completely out of sync (say, in the event of a crash, or you quit SuperSync before it has finished updating iTunes), you should first try to rescan your library. If they seem hopelessly out of sync, you may use the drag-drop method to try to add the tracks to iTunes. Locate the folder that contains the iTunes library, select it and then drag it over the open and running iTunes. Drop the folder on top of the iTunes window and wait for iTunes to complete operations. Exit and restart SuperSync and then perform another rescan.