Well, you have 3 options.
Don't remove the NPCs, and gamble on the game not crashing
Remove all NPCs in merged objects
Identify the NPCs that PTE changes, and only remove those from merged objects (Slooooow process).
It all depends on what combination of mods you are using. Mods really shouldn't be adding/removing items to vendors (like new weapons or armour), but put in new containers that are owned by the NPC. Much safer and less conflicts.
By what you're saying, it sounds like the mod would only affect the inventories as opposed to the NPCs themselves (and that the speechcraft/mercantile changes wouldn't conflict). Correct me if I'm wrong, but would it be safe to run PTE outside a merge with several mods (BTB's mods, LGNPC, Light The Way) that would just affect the NPCs and not touch the inventory?