Coped from https://bugs.chromium.org/p/chromium/issues/detail?id=707181#c9

I narrowed it down a little:

* I backed up and then deleted the "Default" profile folder
* Started Chrome to recreate it from scratch and with everything reset to defaults
* Quit Chrome
* Restored file by file gradually from the backed-up Default folder
* Started Chrome and had a look at chrome://sync-internals after every restored file

As far as my observations go, only the "Preferences" file from the profile causes the problem, if the profile "breaks" local sync.

So for a quick&dirty workaround until a bugfix is released, I am basically able to back up everything except the "Preferences" file; memorize/write down the settings that are important or which I have changed from default values; delete the "Default" profile folder and let Chrome create a new one; recreate all browser settings manually; quit Chrome, restore my backed-up files; voilà, no profile data lost and local sync works flawlessly.

I was able to reproduce this on two machines, so I'm quite positive that this issue is somehow connected to the Preferences file.

Hope this helps anyone in some way!

See coments from https://bugs.chromium.org/p/chromium/issues/detail?id=707181#c9 onward for further context