when the game updates (every wednesdays), it'll look at the pad00000.meta file which kinda acts like the manifest for all the paz files, letting the program know what's where and what needs to be loaded. (I think UndercovertPervert wrote a post explaining this process in detail and better than I can. It should be on the meta injector page I think ?)
If you dont restore backup (of pad0000) through meta injector, it should just get overwritten by the patching process. If all goes well, you launch the game after patch, let it finish patching what it needs to do, then run meta injector to reapply your mods.
If the process gives you an error warning like corrupt file or whatnot, try replacing the pad000 with your backup (restore backup in meta injector. I think restore n patch does all that automatically for you as well) and let the game repatch itself.
If you still get crazy corrupt file error messages, let the game do a file check/repair. It will replace all the paz and files that are not exactly the right size, getting rid of your mods but fixing the game by re-downloading all the necessary vanilla files.
Once that is done, you can re apply meta injector to add your mods and it should work.
If you did some changes within your mods (deleted some files or what not), it is possible that you dont need as many extra paz files as you used to (Meta Injector adds new Paz files from #61337 on (customizable)), and every 100Mb, it'll create a new paz with incremented number.
If your new setup requires less files than before, it can happen that your last paz file(s) is(are) not needed (contains info related to your old setup) and could give rise to error (rarely because paz000 should tell the game that there is nothing to look for in that extra file, but I did have it happen to me once and the error message was very specific, mentionning that extra paz file specifically).
You can delete those last few paz files before launching meta injector to be sure and clean for peace of mind.
So in conclusion, make sure to let the patching process finish by launching the game before reapplying your mods through meta injector. I think that is the most common error I was doing (running meta injector before launching the game). Also, read up on restore n patch, that mini program should help you with future patching processes since it's all automated :)
Hope this helps, good luck and have fun in your modding journey :)
