A master folder i.e. on drive D: “All Documents”.
Within in there are many other folders as well as sub-folders of folders et al.
When I try to sync more than one [other different] sub-folder within the master folder, syncthing warns me of an error that already another folder within the master folder is synchronized.
Why is that and how can I avoid it and synchronize individually various sub-folders and sub-sub-folders within that master folder?
The warning appears when a sub/child folder is shared while one of its parent folders is also already shared.
For example:
D:\All Documents
└── A
└── AB
└── ABC
If D:\All Documents is shared, and then later on D:\All Documents\A\AB\ABC is added as a new share, it triggers the warning because sharing D:\All Documents already included the contents of D:\All Documents\A\AB\ABC.
If you are talking about the “Warning, this path is a parent directory of an existing folder” warning, that is advisory. You can add the folder anyway, but be careful not to share a subfolder with a device that you also shared the parent folder with.
I think some people are missing that the subfolder is not necessarily shared with the same devices as the parent folder.
The original poster didn’t make any such assertion. So I believe the comments assume the OP may not understand the pitfalls of sharing subfolder of already shared folders.