*Facepalm* I have somehow managed to, what I assume, is corrupt my spatial areas because when I try and load them they always load as a different area. I don't know much about this mod so I have absolutely no idea on how to fix it. I don't know if this issue is fixable or not, but any help is appreciated. (Btw, I haven't read many of these other posts so sorry in advance if this question has already been answered.)
Like others have said you have to push the button again to save the data back to the spatial drive before trying to load another area. I found this out the hard way on ME3. FunshineX in his series removed the item transfer pipes from under/behind the machine that move the drive back to the input slot from the output slot - having these pipes there makes it easier to corrupt your worlds because you are not sure if it saved or not. I haven't had a problem yet but I will be doing the same thing.
You can fix your corrupted spatial areas using the instructions in the opening post for upgrades - copying the areas from the template directory to your save game. Make a backup first. You will lose progress in any spatial areas and have to reclear them if you overwrite but it is probably worth it to fix the issue without having to reset all your progress.