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Your website will work fine if you do not upload the _notes folder to your server. The _notes folder is used by dreamweaver, I suggest not deleting it, just don't upload to your server. Or use the Dreamweaver FTP where the _notes folder isn't visible.
If however for some reasons you decide you want to delete the notes folder you can do this without any harm except for loosing important notes etc. etc. If you work with dreamweaver I would not delete the _notes folder.
So you are suggesting to keep it locally on my computer but to just not upload it to the server?
Personally I think that's the best practice.I use notes quite often when building a website it's a very handy tool.
The _notes are just used by Dreamweaver internally but not by your website, so if you work with Dreamweaver keep the notes locally but just don't upload to the server.
I liken the Dreamweaver _Notes folder to the dreaded Microsoft Front Page extension folders _vti_cnf, _vti_inf etc. As long as you're using DWs built in FTP exclusively, it's not a problem. But how often does that happen? If you're like me, I don't want to see any folders or documents in my website that I did not put there for a purpose. In the real world we use project management software or at the very least a spreadsheet to maintain notes for this very reason. If you want my input, kill the _Notes and sync setting in site manager and download a free copy of CleanWearver to get rid of and folders on your local sites. http://www.gnidesign.com/products/cleanweaver/