How do I delete images from the Lightroom Catalog that are no longer on my computer!?

Something went wront on an ingest of my images. I think I tried correcting it by going into my /workingfiles folder were they were stored and deleting them manually. I'm sure I checked to see if I could do it through Lightroom, but maybe I missed the folder they were put in. I am guessing that is what happened so Lightroom still has a small image of them somewhere and will no longer let me re-import them. Any ideas on what I can do to get out of this mess? Thanks.
Image Ingester Pro 3
Lightroom 4.3
Windows 7 Home Premium 64

They are not showing up in Lightroom at all. I already deleted them.
When I try to import them again into Lightroom it wants to add another 2012 folder to wherever I am trying to insert them and then it does the month/day folder when it already has the month folder it should automatically go into and not be adding a seperate 2012 folder first.
I can't even get it to do the above right now. Now all it does is it wants to make this seperate 2012 folder with the month/day folders but has little boxes beside each folder showing that there are no images to import. The images do show up on the import screen but they are all darkened and unchecked. When I click the proper folder to import them they come on bright and have little boxes checked, but that lasts for less than a second before it decides they are not new. They are new images, I deleted them all out of Lightroom, and probably missed deleting some through Lightroom but instead deleted them straight from the folder outside of Lightroom. This is what is probably causing me such grief and I have found nothing in my searches to tell me how to correct this. *sigh*

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