I think I understand why, for most of it.
The pdfs were deleted by the file cleaner plug-in! The plug-in cleans up unused attachments (pdf, png, etc.) not just the empty markdown files. So big warnings if you are using this plug-in.
I am still trying to figure out where my missing excalidraw files went cause they are backed by markdown and they are not empty. It could be caused by some glitch when I switched from icloud to obsidian sync. But I cannot really convince myself how.