Both devices were fully synced indeed.
I tried reproducing the issue with other duplicated folders after confirming both devices were fully synced.
Observations
Folders and files were either moved or deleted on my laptop (multiple times), but some were not deleted on my phone. After I deleted these folders and files on my phone, the folders that again re-appeared on my laptop were deleted.
Sync logs laptop
2023-10-14 19:52 - Server pushed (folder) [Phone] Resources/Fleeting Notes 1/Fleeting Notes
2023-10-14 21:52 - Connecting to server
2023-10-14 21:52 - Connection successful. Detecting changes…
2023-10-14 21:52 - Fully synced
2023-10-14 21:57 - Connecting to server
2023-10-14 21:57 - Connection successful. Detecting changes…
2023-10-14 21:57 - Fully synced2023-10-14 22:07 - Fully synced
2023-10-14 22:10 - Server pushed (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes/Building-Knowledge-Graphs-Practitioner’s-Guide-OReilly-book.pdf
2023-10-14 22:10 - Server pushed (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes 1/attachments/t.daily planner A5.pdf
2023-10-14 22:10 - Server pushed (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes/attachments/t.daily planner A5.pdf
2023-10-14 22:10 - Server pushed (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes 1/desktop (2) 1.ini
2023-10-14 22:10 - Server pushed (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes/desktop (2) 1.ini
2023-10-14 22:10 - Server pushed (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes 1/desktop (2).ini
2023-10-14 22:10 - Server pushed (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes/desktop (2).ini
2023-10-14 22:10 - Server pushed (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes 1/desktop 1.ini
2023-10-14 22:10 - Server pushed (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes/desktop 1.ini
2023-10-14 22:10 - Server pushed (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes 1/desktop.ini
2023-10-14 22:10 - Server pushed (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes/desktop.ini
2023-10-14 22:10 - Server pushed (folder) (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes 1/attachments
2023-10-14 22:10 - Server pushed (folder) (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes/attachments
2023-10-14 22:10 - Server pushed (folder) (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes 1
2023-10-14 22:10 - Server pushed (folder) (deleted or renamed) [Phone] Resources/Fleeting Notes 1/Fleeting Notes
2023-10-14 22:10 - Server pushed (folder) (deleted or renamed) [Phone] Resources/Fleeting Notes 1
2023-10-14 22:10 - Deleting Resources/Fleeting Notes 1/Fleeting Notes 1/attachments
2023-10-14 22:10 - Deleting Resources/Fleeting Notes 1/Fleeting Notes/attachments
2023-10-14 22:10 - Deleting Resources/Fleeting Notes 1/Fleeting Notes 1
2023-10-14 22:10 - Deleting Resources/Fleeting Notes 1/Fleeting Notes
2023-10-14 22:10 - Deleting Resources/Fleeting Notes 1
2023-10-14 22:10 - Fully synced
2023-10-14 22:15 - Connecting to server
2023-10-14 22:15 - Connection successful. Detecting changes…
2023-10-14 22:15 - Fully synced
2023-10-14 22:19 - Connecting to server
2023-10-14 22:19 - Connection successful. Detecting changes…
2023-10-14 22:19 - Fully synced
2023-10-14 22:30 - Connecting to server
2023-10-14 22:30 - Connection successful. Detecting changes…
2023-10-14 22:30 - Fully synced
2023-10-14 22:36 - Connecting to server
2023-10-14 22:36 - Connection successful. Detecting changes…
2023-10-14 22:36 - Fully synced
2023-10-14 22:40 - Connecting to server
2023-10-14 22:40 - Connection successful. Detecting changes…
2023-10-14 22:40 - Fully synced
Sync logs phone
2023-10-14 21:54 - Connecting to server
2023-10-14 21:54 - Connection successful. Detecting changes…
2023-10-14 21:54 - Fully synced
2023-10-14 22:00 - Uploading file Resources/attachments/01 Journals/Working memory/!!Working memory.md
2023-10-14 22:00 - Upload complete Resources/attachments/01 Journals/Working memory/!!Working memory.md
2023-10-14 22:00 - Uploading file Resources/Changelog/Changelog.md
2023-10-14 22:00 - Upload complete Resources/Changelog/Changelog.md
2023-10-14 22:00 - Fully synced
2023-10-14 22:00 - Uploading file Resources/attachments/01 Journals/Working memory/!!Working memory.md
2023-10-14 22:00 - Upload complete Resources/attachments/01 Journals/Working memory/!!Working memory.md
2023-10-14 22:00 - Fully synced
2023-10-14 22:01 - Server pushed (folder) (deleted or renamed) [Laptop] Resources/Fleeting Notes 1/Fleeting Notes 1/attachments
2023-10-14 22:01 - Server pushed (folder) (deleted or renamed) [Laptop] Resources/Fleeting Notes 1/Fleeting Notes/attachments
2023-10-14 22:01 - Server pushed (folder) (deleted or renamed) [Laptop] Resources/Fleeting Notes 1/Fleeting Notes 1
2023-10-14 22:01 - Server pushed (folder) (deleted or renamed) [Laptop] Resources/Fleeting Notes 1/Fleeting Notes
2023-10-14 22:01 - Server pushed (folder) (deleted or renamed) [Laptop] Resources/Fleeting Notes 1
2023-10-14 22:01 - Uploading Resources/Fleeting Notes 1/Fleeting Notes 1/attachments
2023-10-14 22:01 - Uploading Resources/Fleeting Notes 1/Fleeting Notes/attachments
2023-10-14 22:01 - Uploading Resources/Fleeting Notes 1/Fleeting Notes 1
2023-10-14 22:01 - Uploading Resources/Fleeting Notes 1/Fleeting Notes
2023-10-14 22:01 - Uploading Resources/Fleeting Notes 1
2023-10-14 22:01 - Fully synced
2023-10-14 22:10 - Deleting remote file Resources/Fleeting Notes 1/Fleeting Notes/Building-Knowledge-Graphs-Practitioner’s-Guide-OReilly-book.pdf
2023-10-14 22:10 - Deleting remote file Resources/Fleeting Notes 1/Fleeting Notes 1/attachments/t.daily planner A5.pdf
2023-10-14 22:10 - Deleting remote file Resources/Fleeting Notes 1/Fleeting Notes/attachments/t.daily planner A5.pdf
2023-10-14 22:10 - Deleting remote file Resources/Fleeting Notes 1/Fleeting Notes 1/desktop (2) 1.ini
2023-10-14 22:10 - Deleting remote file Resources/Fleeting Notes 1/Fleeting Notes/desktop (2) 1.ini
2023-10-14 22:10 - Deleting remote file Resources/Fleeting Notes 1/Fleeting Notes 1/desktop (2).ini
2023-10-14 22:10 - Deleting remote file Resources/Fleeting Notes 1/Fleeting Notes/desktop (2).ini
2023-10-14 22:10 - Deleting remote file Resources/Fleeting Notes 1/Fleeting Notes 1/desktop 1.ini
2023-10-14 22:10 - Deleting remote file Resources/Fleeting Notes 1/Fleeting Notes/desktop 1.ini
2023-10-14 22:10 - Deleting remote file Resources/Fleeting Notes 1/Fleeting Notes 1/desktop.ini
2023-10-14 22:10 - Deleting remote file Resources/Fleeting Notes 1/Fleeting Notes/desktop.ini
2023-10-14 22:10 - Deleting remote folder Resources/Fleeting Notes 1/Fleeting Notes 1/attachments
2023-10-14 22:10 - Deleting remote folder Resources/Fleeting Notes 1/Fleeting Notes/attachments
2023-10-14 22:10 - Deleting remote folder Resources/Fleeting Notes 1/Fleeting Notes 1
2023-10-14 22:10 - Deleting remote folder Resources/Fleeting Notes 1/Fleeting Notes
2023-10-14 22:10 - Deleting remote folder Resources/Fleeting Notes 1
2023-10-14 22:10 - Fully synced
2023-10-14 22:19 - Connecting to server
2023-10-14 22:19 - Unable to connect to server.
2023-10-14 22:22 - Connecting to server
2023-10-14 22:22 - Connection successful. Detecting changes…
2023-10-14 22:22 - Fully synced
To see if I would get the exact same copy of my vault on my tablet, I also enabled syncing PDF and audio, which were not synced before.
(For some reason syncing stopped a couple of days ago on my tablet. I was still logged into my account but had to select and unlock the vault to start syncing again.)
Syncing completed and many folders and files re-appear again on my laptop.
Audio I moved from a resources sub-folder re-appeared there on my phone, but only the folders came back on my laptop.
What would be the best way to prevent duplicates?