App updates lead to merge conflicts?

[Frederick888]

I think I get false positive merge conflicts due to app updates, so I'd like to confirm if my theory is correct.

What happens is

1. I log into Notesnook, web for example
2. NN tells me it needs to update
3. There are suddenly a bunch of conflicts afterwards, although I never updated the same note on different devices simultaneously

I suspect what leads to these conflicts is that during an app update, it also migrates some outdated local note data, which marks them as modified, so they end up conflicting against their remote copies.

If I'm on the right track, I wonder if we can do things a bit differently. For example, just thinking out loud,

1. After a note is synced, mark it as 'synced' locally (I guess we already do this?)
2. App update starts
3. Overwrite local synced notes with their remote copies
4. Migrate data
5. If the app is now the same version as the one that wrote to the remote copies, they naturally don't need to be migrated again; if the app now is newer, since the migration is done on the latest data, we just sync them to remote directly

If I was wrong, I wonder what is actually happening instead? I usually use NN on my phone so it's extremely common for me to see lots of conflicts when I log into web from time to time.