The first rule of a second brain is to not lose any content. People, of which I am one, make mistakes. Those mistakes should be correctable. Even if the correction process is clumsy. When the tool fails at this our confidence in it is lost or greatly diminished. This is what happened to me with Obsidian and iCloud.
After several months of use it was clear that I did not use folders in Obsidian. I found that if I named notes well then the open command's search feature was often all I needed to locate the note I wanted. To locate others a full text search with a broad context tag (like a project tag) worked well. So I eliminated folders.
Before removing the folders I went through the notes to improve file names, add tags, and sometimes add useful search terms. I then moved the files out of the folders into a "notes" folder. (I do still have "notes", "attachments", "daily", and "templates" folders.) Once all the notes were removed from the folder I deleted the folder.
All the movement and deletion was done within Obsidian. The reason I used Obsidian to do this, rather than use the Finder or the command line, was that I was unsure if Obsidian needed to "know" about these changes. Its internal workings are unknown to me and so this seemed like a responsible method.
I made a mistake and deleted one folder that was not yet empty. I did not discover this until a week later when, back at work, I needed a note that happened to be in that folder. It was gone. I was horrified as this note had the details of the sequence of intricate steps needed to build, configure, deploy, and use an internal server. It was the only copy I had. (That this information was in my personal notes is a story for another time.)
You would think a software developer with decades of experience with version control systems would never let this happen. But I did. And I did because I have become perfunctory about some matters of personal file storage. A file deleted in the Mac goes in to the Trash, Dropbox retains deleted files for 30 days, and my local storage is backed up at Backblaze. Losing files is kind of hard. Unfortunately, my Obsidian vault was on iCloud.
iCloud has a 30 day retention period for deleted files. For deleted files to be retained the deletion must use Mac specific SDK methods. (I am speculating here based on behavior.) Obsidian does not use these methods. It manipulates the file system as any other POSIX application would. Once a file is deleted it is gone, effectively, forever.
This loss did shock me more that I would have expected. I think part of the reason was because I had been considering moving my local storage to iCloud. That is no longer a consideration.
As to Obsidian, I have grown less excited by it over these months. Its document editing and linking are rudimentary. Its plugin community is very active right now, but that is unlikely to continue over the long term needed by a second brain. Lastly, Markdown is an intentionally limited and ultimately weak markup language. Until I find an alternative, it is the better of the free solutions.