Bolivia? No worries. Chile? ...
If you return to Chile you can expect the aduana to bring up the fact the bikes weren't signed out - their system is computerised, Chileans are organised & they're not just going through the motions at the border. That said, in my experience they were always very reasonable & if you're on the bikes so they can see you still have them, then returning shouldn't worry you.
If you're not planning on riding back to Chile then maybe check in with their consulate when you're home to see if there's something you can do to prove the bikes left the country & formalise the situation. Chile's great - would be a shame if you had problems returning there in the future.