Just wanted to chime in that I too had another problem with Shadow of the Tomb Raider after getting around the 72% copy progress issue. When I went to build the packge I saw this "Format of the Param File is not Valid".
I figured out what the problem was. I had installed patch ver 2.00 from orbispatches. Looking at the change notes I saw this "Full game remaster in order to fix memory and loading issues due to the high number of patches since the game launch". So it looks like after enough patches the dev's mark it as a remaster which probably supersedes all content from the base /disc. I deleted the game data and instead installed patch 1.19 which worked flawlessly.
You can also try using orbis-pub-sfo to un-check the "remaster package" box but when I did so and saved I was treated to another error. Going with a lower patch version was an easier way to fix it and I honestly didn't notice and difference in the game's performance.