The in game default passive will stay written in the armory, and unless you swap the default passive out for another. Unless you are referring to something else, please let me know.
Good,but unfortunately wont work if you use the shodan stat editor as shodan overwrites the passives and must be installed AFTER the editor as trying before tells you to restore backup with the armor
Im using both together without this issue on my end, so there may be a difference in our versions or install order.
Which Shodan version are you using, and which program are you clicking Install in first? Also, does installing Shodan actually remove your custom passives in game, or does Armor Workbench just show an error afterward?