First I want to clarify the symptom. It's not like the bookmark entries are duplicated under the same folder, but whole folders are being duplicated.
The duplication problem has been on and off since the beginning of the sync feature, but this time it's worse than ever -- more and more duplicated folders are being created and it's quickly becoming a disaster -- please help!
I have 3 PCs and one android client. The PCs are running the latest dev builds, and the android client is the latest dogfood version.
A month ago I get two copies of each folder so I fired up the deduplication tool, and then manually merged the remnants (the tool does deduplication, but doesn't merge the folders).
Then a few days ago I start to see duplicated folders again, so I removed sync profiles from all but my primary PC to do maintenance in an isolated environment. I again run dedup tool, and then manually cleaned up the duplications (that's a lot of folders). According to edge://sync-internals all is well and it's communicating with the sync server in batches.
I then created new profiles on the secondary PCs and the android, hoping they'll catch up with my primary PC.
Today it started syncing on one of the secondary PCs and here's what I have:
As you can see in the screenshot, each folder has 1 to 5 copies, and the content of the copies are not identical (e.g. one folder missing this, another folder missing that) so even the duplication is not consistent.