Edited Coalesced.ini lead to inability to use Normandy upgrades and unpreventable death of crew members

Okay so the issue is, I pulled out an edited Coalesced.ini from the internet to function as a trainer. It allowed several things such as speed increase, boosting renegade points/ paragon as well as removing them, it granted god mode as well as unlimited ammo, all that good stuff. The thing is, it also grants all the upgrades available in the game, which seems to have caused an issue. Even though I have those upgrades, when I attempt the last mission, the "Suicide" one through the Omega 4 relay, It acts as if I do not have any of the ship upgrades to prevent the 3 crew members that die. This really friggin sucks cuz I don't want anyone to die on this mission and I know that is a complete possibility from research. I know there are plenty of other people who have used this exact same trainer, and I'm hoping someone with that experience can be of help to let me know what they did to fix that bug. Something of note would be that I noticed I had to "re-buy" some upgrades on the terminal, even though they would say eg: Ammo Piercing upgrade 7/7, and I would simply repurchase them until they disappear from the options. I simply did that for everything I could until all that remained was the respec talents and that other thing that always remains as well. I was never given the option to upgrade the Normandy, it remained grey no matter what. I attempted to speak with all the crew members for the upgrades, and when they opened there upgrade tab, everything remained grey and after I closed it, they acted as if I never purchased anything, which is the case. I also restored my original Coalesced.ini to see if that edited anything, but to no avail. I remained unable to change anything and I end up losing Jack, Thane, and Legion in the firefight.