It worked for me to get rid of the extra chapter saves. I don't mean other saves in the main save folder - I mean chapter .sav files inside a specific save folder, for example: C://user//GogGames/NWN Diamond/saves/007-MYSAVE .
Inside my 007-MYSAVE folder, there were .sav files for both Prelude.sav and Chapter1.sav . I got rid of Prelude.sav, and then MYSAVE started showing up in the game's load screen again.
I'm expecting the problem to return once I reach Chapter 2. I'll likely have to get rid of Chapter1.sav .
A few times, the old chapter saves have spontaneously reappeared in all my saved game folders, and I have to keep repeating the process.
It's irritating, but I can work around it and keep playing at least.
I had the same problem and your method worked for me I was at the end of chapter two Thanks.