The only thing hat is synchronised between app and website is the activation date. And you don't need to activate your pass to book reservations.

Additionally, it's often cheaper to book elsewhere than via the Interrail website, since Interrail have a 2€ booking fee for every reservation, and optional reservations can be much more expensive (6 or 8€ per train) than via DB (4.5€ per journey) or CD/ÖBB (3€ per train). See this topic for more information:

Any trips you create on the website are  totally separate to the trip you create when you add your pass to the Rail Planner app. Both of them are fundamentally planning diaries, and like any diary they can be added to and subtracted  from at will.

The key ”trip” is the one you have on the planner app on your phone - that is the one you transfer from to your pass the trains you are about to board, and that becomes your ticket to travel.

Reservations are rarely linked to specific passes and are in fact totally separate from your pass. They are never tickets to travel without a valid pass as well. 

You can add additional passes to your device or onto separate ones, depending on your personal preference, but once activated they cannot be removed from that device by the user, only by customer services.

You can buy reservations for multiple people with one pass and then each passenger needs to produce an appropriate valid pass on the train.