nvim_win_set_config() changes the position of the windows

[MLFlexer]

In the function change_instance the window config is changed. I would like to use

vim.api.nvim_win_set_config(self.output.window_handle, self.output.window_opts) 
vim.api.nvim_win_set_config(self.input.window_handle, self.input.window_opts)   

However this lowers the placement of the output window, and thus I have resulted to use a double call to toggle as a temporary fix for this.