but than how do i remove all the photos that are on iphoto????
File -> Export
To export Event by Event or Album by Album check out *_[iPhoto to Disk|http://www.iphototodisk.com/index.html]_*
Averaged out of the cost of iLife, iPhoto is a $16 app. For that you get a lot, but not everything. It definitely works best with a Managed Library (and from your description of your issue, you're running a Referecenced one?) stored on the local Mac.
If you must have photos spread over 5 disks then you might consider having 5 managed Libraries - one on each disk. That will avoid all these issues.
Other than that check out Aperture which is far more flexible at dealing with these kinds of set-ups, and will easily migrate your iPhoto set up.
Ok so I know this post is very old for me to be answering now, but it's still one of the top hits on google for "fixing broken links in iphoto."
Anyway, so I had the same problem where I deleted numerous photos from my computer. (slideshows I've made for friends) Yet their thumbnails were still showing up in iPhoto like they still existed. Making it difficult to see which ones were technically broken wasn't until I previewed the image in full frame by hitting space-bar that iPhoto would prompt saying "photo is missing"
So as I was searching my iPhoto library files looking for duplicates I found the thumbnails folder. For some reason I thought these were duplicate photos so I deleted them all, which turned out to be a helpful trick! Because upon going back into iPhoto, the program began re-creating all of the thumbnails I just deleted. Which turned out to be a great work-around. Now the photos that were broken appeared as empty grey squares. Figured I'd just to pay it forward and possibly help someone else.
iPhoto '11 9.4.3