WhiteNoise, thanks for all your replies.
Files and folders actually exist on my local disk as they’re created locally (as opposed to created somewhere else, synced, look like it exist, but sync service saying “there are sync-able files on the cloud.”)
Other sub-folders include personal notes, so maybe I should do the following first: uninstall, make sure config files and info are wiped, make sure Markdown folder doesn’t contain Obsidian related files, and see if the problem still occurs. If it does (i.e., still missing sub-folders), I’ll come back here.
Thanks again for all of you who kindly replied, and also for the developers who are creating this cool software!