Dont get worried. Whatever you change all you have tot o is change it back into normal parameters. Personally I dont know a huge amount of pc coding and all that stuff. But pc expansions are the same. MOST likely if you changed something simple like extra resources, the expansion aka sequel wont really care, because it wont read it. Like ME2 if you got 9mill credits, all the game reads is you got above 1 mill..... thats it.
You dont have to replay the entire game... unless you want to out of kicks. But simply revert anything you did back.
Resources:
Load a previous unmodded file and look at the amount of resources you had at the end, and then go put something similar to the modded file, i Have 300k left after ending the game, when ME3 I will put something between 30k to 60k in each.
If you placed weapons in hands of allies that aren't theirs, like me avenger to jack or geth rifle to tali, simply change them back.
Credits, same thing.
The game wont care what you have most of the time as long as you dont go nuts. Now they said "maxing abilities" MIGHT mess up your game... well simply copy that file, have normal points added, and another save where everything is maxed, if the game doesn't export properly then thats fine, if not then have fun with maxed out features.
Personally I been doing the exploits of ME1 recently coz Inever even knew they existed, on infinite creds of reloading save files, which also gives you infinite exp. 1 playthrough I was lv 60 already.
Did the loriq quinn thing for paragon renegeade.... ME2 file was fine being imported from that "potentially corrupted glitched".
Now is there a 100% chance like Darth mentioned that the game will work perfectly.... no. But is easier now with USB drives, just make copies of the same.
Once I am done with a character, I go back to a folder, there is a folder with the career heavily modified, and then I quickly make copy revert everything back. I know my Vanguard lv 30 with 9999heat sinks for the revenant, every skill maxed. ALl pistols replaced by Assault rifles with those who have shotguns, and those who hold SMG's hold snipers.
I have a copy of that file where everything is normal, not all skills maxed, no clips modified, no extra weapons.
If my heavil modified save doesn't export correctly, I'll try its mirror pure copy.
IN the end, just make copies, revert anything you change to normal parameters and you'll be fine.
I've.....acquired free dlc's from my friends via liscense transfer and all my modded files work perfectly.