I have a folder on my external hard-drive with all my Tiffs and my geodatabases with my Mosaic data sets. What is the best way to move this from my external to works drive? I am afraid that all the links will get broken and I have to start all over again.
You may want to examine the "Repair Mosaic Dataset" geoprocessing tool. It allows you to redefine the new path for the moved raster datasets within a mosaic dataset.