Aha, I finally figured out what I did right and what I did wrong, so accidently wrote some bad code, and the game while loading the server just kinda deleted part of it and made it new (kinda like steam validating files), anyways, this caused it to also overwrite the save file, and unknowingly forced the game reload a percentage of the chunk in the region, which is what actually loaded in my prefab, although only 20% of it.
Anyways, what you have to do, is somehow force the game to update the chunks and or region where you want your prefab to be placed, and it fully updates that region then your prefab gets placed into the world completely. There's a few ways to do it, but a very simple one which worked for me was to simply delete the region, and let the game regenerate it with the prefab loaded in. You wanna know your region first though, to do this you go in world (or in server) to where you want to place the prefab, then press "F3" then click the "CH" to get know the region you are in, then go to your "save file" NOT the "generated world" one and delete that specific region. Provided you have your prefab situation figured out, deleting this region from the save file and having the generated world file with the prefab will cause the prefab to be generated into the save file. and Bam, you can basically copy paste from one world to another. So all in all you're gonna wanna do a bit a both, the tutorial in the comments above, plus a the few extra steps I did. Here's a link explaining the region updating better: