I kept messing around with NCS Expert and I think I found what I was doing wrong.
When starting NCS I always made sure to delete the fsw_psw.man file from the working directory for fear of coding the wrong file to the car somehow. However, I found that when loading a profile with .man manipulation enabled without a .man file in the working directory I'd get an error and wasn't able to continue. So to get around this I was using the Expertmode profile to read the desired ecu and get the fsw_psw.trc file. Then I'd make my changes to that file, save the .man in the working directory, and switch to the "fsw psw man" profile to continue.
I guess switching profiles during a session causes another .trc file to be pulled from the car and this was the source of my problem. I guess the "coapiReadSgGetFswPsw" command compares the .man and the .trc files in the working directory, but because I was switching profiles in between the read and attempt to write, my files weren't the same and thus an error was generated.
If I'd followed xxxjecxxx's guide more closely I wouldn't have had this issue.. I guess because I don't completely understand this software I was trying to be cautious but it ended up causing some problems.