Syncing does not usually change the colors assigned to existing calendars in SOHO Organizer or iCal. The only exception is if Sync Services has either product delete and then re-sync everything (this is called a 'pull-the-truth' sync and usually only occurs if you reset your sync history using the advanced preference in iSync). If a 'pull-the-truth' sync occurs, then SOHO Organizer and iCal will regenerate random calendar colors as it recreates each calendar.