The custom botany pots do not work in a server, they revert back to the original non custom crafts e.g coral giving coral, it not accepting iron and stone

I think that is probably because you don't install the server pack correctly

I transferred the libraries, mods, config and defaultconfigs (alongside doing without defaultconfigs but nothing changes) and the jar file with renamed forge, im unsure if im missing a file because the server runs just not the pots custom data

openloader folder?

That fixes it thank you :) tutorial only showed 3 folders