Did you test it out yourself before pushing it to live? If the file is being deleted because of an installation of a new version, that seems really bizarre. I'd hazard a guess that it may have to do with the file locations. In which case, you could just push an update (after testing, lol) that searches for the old ini file when it's first booted (how you do this depends on how you were saving it in the old version) and then perhaps copying across the data to the new ini file or something similar to that. Then just make a mark in the new ini file saying that you have found the old one and imported the data and have the game not search for the old ini file if it finds that mark in the new ini file. I doubt the data has been completely lost, but it would be very unfortunate if it were.
I have had to do stuff similar to this a few times as I've been building Spaceslingers and have updated various things within the map editor; finding old files, importing the data and updating it to comply with the new data format. It's not a super hard thing to do, just spend some time experimenting and testing.