Emptying the trash can in iphoto causes the grey exclamation point.

Shortly after buying my new mac I made the cardinal error of manipulating some of my photos directly through finder, and ended up totally messing up my iphoto library. It's basically fine now, after much heartache - and I back up disc copies regularly and I also use time machine now. However, the other day I noticed there was a ridiculous amount of photos in my iphoto trash can - so I emptied the trash can in iphoto. I immediately got the grey exclamation point of death back in probably one third of my pictures. I restored the library from time machine, and the ex points went away, but does this mean that the link is bouncing THROUGH my trash can to get to the file? Is there any way for me to safely empty that trash can without having to once again rebuild my photo library?? (I'm a total shutterbug and don't want or need that hassle...)
I'm running the new iphoto 09 - but the problem was there before I installed the upgrade.
Something tells me OldToad is going to reply to this one... (At least I'm hoping...)
Thanks for any and all input.

Well hello, Old Toad, thought you might find us.
Terence, last night I backed up my library in time machine, emptied the trash can in iphoto (took five or six attempts, iphoto kept shutting down) and then rebuilt the library. Just an fyi, when I said ridiculous amount, I meant it - there are 26000 plus photos in my trash can. (I know why, but I think it's unimportant to this issue).
When I rebuilt it found 13000 plus photos to reinstate. I said ok, and around three hours later it was all said and done. No change, I still have the grey exclamation point of death on about a third of my photos in the events. The reinstated photos are all in an album, not an event - I can't seem to move them from the album into an event, and there aren't a lot of them there anyways that I'm all that attached to.
SO...
I restored the backup copy from time machine. Tonight, I will try OldToad's recommendation and try to put these photos back into their original homes, but with that many pics It may be Tuesday or so before you here back from me...
Wish me luck, thanks SO MUCH for the suggestions, and I'll keep you posted.

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