I opened the file and exploded some of the blocks. In the image on the left, the grey parts are the blocks that I exploded. Then I ran Flatshot and got the image on the right.
As I was exploding blocks I found that some blocks are inserted twice, so there are duplicates that are overlapping. The model needs to be cleaned, to remove all the duplicate overlapping blocks.
As for exploding blocks, I only had to explode some of them to get Flatshot to work, so I'm not sure what the problem is. Maybe there are some bad blocks? A lot of the blocks that I exploded were mirrored. Maybe that's an issue? Maybe copy and rotate would be better than mirroring? You will have to experiment to find out what the root cause of the problem is. In the meantime, exploding the blocks seems to work.