Well if you didn't edit the .ini again after you deleted the other one ... it will definitely crash if you have more than 2 cores.
This fix ...
Open up the fallout.ini file in: My Documents\My Games\Fallout3
Find the line:
bUseThreadedAI=0
change it to:
bUseThreadedAI=1
Just hit enter with the cursor at the end of that line
Then input this line at the new cursor below that line:
iNumHWThreads=2
Close and save the text box:
This will limit the game to 2 cores and prevent the engine bug from causing the game to freeze.
However you mention you have the GOTY eddition ... which comes with GFWL. And what your describing sounds like windows 10 is launching the opposite of what you usually played with. There are 2 different save paths ... one for off line and one for logged into GFWL.
So look inside your saves folder .... does it have another folder ?
Or did you do a file search for ".fos" files ?
Were there any other locations they were showing up in? .fos is the extension for any Fallout save files.
Add edit : sorry the link fix wasn't up to date , so I just pasted the info.