Thanks for the reply! I was about to make copies of my Joplin profile before trying to restore the .md files, when I noticed that the Simple Backup Plugin did indeed make a copy (just not where it was supposed to, i.e. the path I specified, but in the Joplin .config folder). So a big thanks to the dev of that plugin! This unpredictable behavior has indeed saved me many hours.

General comment: I think that Joplin's lack of a "trash" folder should be grounds to proactively ask users if they want Simple Backup installed when they start using Joplin.