Originally Posted by
Xesyliad
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You will need to find someone who hasn't yet completed those side missions and then join their group, ask them to leave which should leave all their active missions on your session, allowing you to then go and complete them again collecting any missing echos. At least that's how I was able to go back and collect them again.
I would recommend matchmaking a normal mission in the zone with the missing echo which should put you with someone who most likely hasn't complete the mission yet.
The other alternative if you have friends, is to make a fresh character, ask your friend to join you once you have gotten to Manhattan, ask them to travel to each safe house so you can fast travel to them to read each bounty board revealing the side missions. Once the mission with the missing echo is available, ask your friend to start it, you can then switch back to your main character, join them again, complete the mission collecting any missing echos along the way.