I've been doing the same thing as you with updates, use a vanilla folder for updates and them move back to the LSPDFR install.
I'm getting the same 7002.1 error on the launcher with my version, 2944. Same issue when I switch to my Liberty City version which is an even older version, 2845. But, when I move back to the vanilla folder, it launches.
I have a feeling with the new update there is something missing on the older versions that the launcher is looking for.
Still looking for a solution, but might just have to spend a day trying to update everything if nothing new arises soon.