Still having this issue? I haven't personally stumbled across this issue so far, but from what I see it's not related to BC, but to permissions over the respective file/folder, which can be tackled by disabling the option to "Maintain Synchronization Information": http://prntscr.com/3tz1lh, from Site Definitions, under Remote Server.
Hope this helps!
I am having a similar issue but only for files in sub directories.
Every time I am opening a file for example \\wwwwroot\sub_folder\index.html I am getting the same error message.
However when I open a file in the parent directory I am not getting this error \\wwwroot\index.html.
My local files are not actually stored on my local machine but are stored on our domain server in my users documents folder.
I have tried showing the hidden folder and files to locate the _notes folder and delete it along with the dwsync.wml then closing and opening DW but there is no such folder created to delete.
I have also turned off Maintain synchronization information and I still get the same error message.
I do have a test server but not a remote server setup.
I have the test server setting to automatically push filers to test server and always suto save dependent files.
But every time I open or make changes to the index.html pay with my sub-directory \\wwwroot\sub-directory\index.html I get this message appearing.
It does not happen with any of my parent directory files.
How can I stop this message appearing without having to move my files from my domain server user folder onto my local machine disc drive?
Well I didn't have the time or the patience to wait for a response and ended up placing my website files on local disk drive. This allowed the dwsync.xml file to be created and has fixed my problem. However I would prefer to have the files on our domain server as this is automatically backup and my local disk drive is not.
But anyhow. I have solved this problem myself.
But it doesn't explain why the parent directory files manage to create a _notes/dwsync.xml but the sub folder wasn't able to create the same folder and file with the server domain user folder.