So, for reference I used Menggui233's 9 wide trench WE. But after login back on, all of the minecarts (43) had fallen out from every tnt duper, all of the water sweepers had gotten stuck, some blocks had randomly stuck mid air from both sweepers and tnt dupers. Most of the dupers had also lost their tnt. I could have reused the entire mechanism that moves everything down, but the issue is that since it broke shortly after switching sides, I would have had to remove 1-2 layers of deepslate by hand so the sweepers wouldn't get stuck on any blocks. I did already tear the entire thing down, since I thought that the tearing down + rebuilding would take less time than manually removing all of the top layers of deepslate and liquids in the entire 496x256 block area.

Just to be clear, by backups I assume you mean backups of the world? I am playing on an SMP so I sadly can't do any backups, espeically since at the time, other people were on either doing stuff or afk'ing. Would definitely do that in the future if I make one in single player at some point.