Added mod to server mods list, recipes show in JEI, but when crafting in crafting bench no resulting item shows up.

in the logs there are no related recipe errors, but on the first start there was some block ID issues

Are you able to /give the items via command or does that error too?

no, that works

I have tested it happens when you add subtract mods in the process of running the server

As I understood, forge is not particularly good with hot-swapping mods, even if they do not affect the world or existing blocks, so I guess there is no issue with the mod, just forge in general.