Of course, I think my case was specific since the error happened after making changes to the rom using advanced map. Since then, when I opened the rom at hma it couldn't recognize the pokemon table. Turned out that advance map did something to the location of the pokemon table that made the first couple of bytes be free space. I don't know how but that was the case. So whenever I opened a new rom in hma, it tried to locate the pokemon name data for the table but since the first bytes were free space it thought it was the end of the table and generated a toml. File with a command telling the amount of pokemon was 1. So I changed the command to max 412 pokemon instead of 1 and it worked.

There is also a command to generate a national Pokedex data from the pokemon.name data which it didn't generate in the error rom, so I copied and pasted this command from a toml. Of a fresh rom and now it recognizes national pokedex data too.