Which mods are you talking about? According to the log, you might had the twilight mod while you were running forge and using the same world in vanilla is just not possible
I added all the mods at the same time, so if biomes o' plenty was successfully removed but not twilight forest, idk, but I never actually opened the server with the mods on it. Maybe it has something to biomes o' plenty only generating when going to new chunks, vs twilight forest creating a new dimension. Is there a possibility that I can find something in the dimension folder to delete to fix it?
Edit: Is there also a specific file I could manually edit to remove the missing entities?