Why does has my large photoshop file now have blocks missing from layers?

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I'm have been working on a large file 1.7G and it was working fine, if a touch slower than normal. Then I added a layer and it had a square cut out of it. I restarted the computer and I found the file then had loads of squares and rectangles cut out of lots of layers. Any idea what this is? I'm hoping not to have to re-design the whole thing. Thanks.