Yellow triangle appears on all photos but no problem found?

Things have definitely slowed down on Aperture since I upgraded to a Nikon D800 (each raw file is about 40mb). I'm having problems with speed and occational crashes. Yesterday the computer (macbook pro, 3 years old) forced me to shutdown and when I restared I had to rebuild the library which finally opened and showed ALL my images in Aperture had the yellow triangle with "!" and the arrow. I've had this issue with some files before and would "locate referenced files" (I keep all masters on an external which is backed up twice in differnt locations). Locating referenced files has always fixed the problem but here's the issue, sorry it's taken this long to get to it.....
When I locate files they are found quickly on the external drive but the button to reconnect (tried 'reconnect all' too) doesn't do anything. I then finished all my edits from the last shoot and exported without any problem. So it looks like it's all working fine but I'm confused/nervous about those **** yellow triangles that are on all of my 17000 images.
One thought is that I may have had my second external plugged in still after I had done a manual backup... and maybe Aperture referenced the backed up files? Even if that happened I should still be able to locate referenced files on the master hard drive and reconnect all.
Any thoughts on this would be appreciated.
Cheers
Pete

When I 'control/alt/clicked' and chose "repair database" in Aperture, it quickly said there was a problem and I had to "Rebuild the database". I first quit, and made a backup just in case, then went back in and chose the "rebuild" option. IT WORKED. All the yellow triangles are gone and it even fixed a couple of the glitches with exporting I was having.
Thanks for your guidence Kirby and hope this helps others.
Pete

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