Indeed the book "The Last Eleven" has many of the answers, probably as much as can be found after so many years. Some Car ID's are missing and the relevant cars are numbered 1-11 (hence the title), whereas only a few chassis numbers are known, and the book also clearly states that identification is not 100% sure.
There was never an intention of entering 4 cars at Le Mans, quite likely Porsche intended to send only two. Two cars (#1 and #10 in the book) were indeed crashed in the months before Le Mans and the remains were used to build up a new car. The book suggests that it was a new car (chassis/body) taking only some running gear of the crashed cars. That was one of the cars going to Le Mans, while the other one was another car, unconnected to the previous dramas. These were 2 of the following cars #2 (356/2-054 - 3001/A), #3 (356/2-055 - 3003/A) or #11 (356/2-063 - 3002A). It is also not clear which of these two was the one that crashed in practice. In the end only one car started.
One thing is sure, the four cars involved never existed all four at the same time. Two at the same time for sure. Three at the same time possible, but then not sure if there were 3 cars earmarked for Le Mans, or that there were never more than 2 at the same time.
Maybe other sources can add some information that helps to unravel this puzzle. At least we have a nice starting point now.