@JackOats Part 7 of the "quick guide"
The theory is that you save main.pd to save the work you have done building the modules into a working project.
AND then click the little save button on the left of main.pd to save all the settings that you have made within the modules. (They should then be saved in /patch_editor_abs/stavestate within the folder containing the main.pd that you are using.)
Looking at Part 9 you should delete basic-osc.pd from the bin/extra folder where you copied it yesterday..... or you will have the problem it mentions.
I hope the main.pd will still work when you have done that (quit and restart Pd afterwards).
When you open main.pd again do it by double-clicking the patch.
Don't do it from the Pd file menu, because you will not know which main.pd from which folder you are opening.
AND always completely quit Pd before starting work on another main.pd or Pd will remember to use the first one you opened........