So I have now run into this problem over and over again now. I will change the size, or the rotation of one of my prefabs. I then click save and it seems to keep the changes. But once I hit play and run the game it will go back to what ever I just changed. I have also tried setting it to auto save, and tried dragging the object into the scene, deleting the prefab and recreating the prefab using the one in the scene. And it is the same thing over and over again. This is really starting to stop me from being able to get my game finished. So if anyone has seen this before please help!
I updated to Unity 2022.3.40f1 and it fixed it