Remove Orphan blocks from "personal" blockchain
It is basically impossible to do what you want without verifying the blocks yourself and constructing the chain status yourself. The easiest way to do this is to run the client that downloaded those block files in the first place as it will know the chain status to be able to construct the main blockchain. This piece of software has the server that the linearize script interacts with. So just run that with the linearize script and it will construct you proper bootstrap.dat file.