Some more thoughts:
a) Maybe I have overlooked it, but have you tried a setup without Dropbox? My approach to debugging an Obsidian vault typically starts like this:
- Create a new local vault on my Mac. Make sure that it is in a location that is not being synced with any cloud. (Depending on your MacOS settings, MacOS might be syncing Desktop and Documents folders to iCloud without you noticing it.)
- Use Mac’s Finder to copy some of files from an external source to the new vault. See how Obsidian handles them. Then add more files. See how Obsidian handles those. Repeat until all files are copied to the new vault.
- Only when I’m sure that Obsidian can process this vault offline, I start exploring sync options.
b) Explore sync options with smaller vaults. Does Obsidian work at all with Dropbox? Obsidian can’t access Dropbox servers directly. So it works with a local copy that is managed by Dropbox’ official app or some other apps that you might use to sync Dropbox servers with your devices. There’s a lot that can go wrong here, even with tiny vaults.
c) Number of files. In my experience Obsidian can handle 10K files easily. But I don’t recall any success story that involves 100K files or more.
d) File names and types of files. Obisidan seems to handle some file names and some types of files better than others.
e) There’s a feature request that addresses the use case of large folders with mixed data. Many problems should disappear, if it were possible to exclude certain file types, file names or whole folders from indexing: