If this mod auto-generates a name identical to the name of an existing entry, it just erases the old entry even if they're different ores.

This is happening to me because I use Angel's Infinite Ores, which puts a patch of infinite ore at the center of any patch of normal ore. Since they have the same coordinates, YARM just erases one to list the other.

I know I can manually rename each entry before recording the next but I wanted to let you know there's a conflict here |3

It's definitely recorded the known issues, but it hasn't been a priority. I'll reply back here when it's fixed, or you can subscribe to the Github issue.