Character advancement with custom modules
I've seen related questions but nothing that directly answers this: will selecting a class from a custom module mess up advancement of prior levels came from the PHB?
I have several custom modules, some with archetype options, that I can turn on and off depending on campaign. I have a player that took two levels of monk using the PHB data. Now, at 3rd level, they've decided to choose one of the monk Ways from one of my custom modules. I'm of the impression that this will show up as Monk2/Monk1, yes?
If so, is there an easy way to fix this?
Is there a way to prevent this in the future? It doesn't make much sense to dump all my custom content into one merged module because then I can't selectively turn parts off. I also can't force players to select a level 2 or 3 archetype at level 1 character creation.
TIA for the advice!