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I think it is not limited to Obsidian sync. According to my experience, the "Show files from subfolders" and "Exclude files/folders" options do not really work any time a new file appears (for example, when an image is pasted and added to the vault, it is displayed as a file even if it shouldn't be). This applies to both file view (bottom pane) and folder view (top pane) - that one also shows "excluded" folders when they are created.
Also, the options "hide attachments folder" doesn't really work either because it should respect the Obsidian setting of the name of the attachments folder, not used hard-coded "attachments".
New sub-folder files are added to the file list pane while sync is occurring, even when
Show Files from Sub-Folders
is set to filter them out.Once synced, clicking the button twice to toggle the filter off and then back on is required to hide the new files.
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