Scan Magic

We are progressing with FCSvr implementation and doing fairly well. Apparently when setting up I enabled 2 complete scans, one of the "Media" device and one of an external 1T Raid. Of course this quickly brought processing to it's knees by completely rescanning the external hard drive every night and replacing every asset. I have disabled both scans. The external drive contains hundreds of random FCP projects, photographs, render files etc etc, all of which are now faithfully cataloged in FCSvr. Should I simply search by file type and delete?