Is there any way to view audit logs when a file in the file cabinet was deleted? I have an image file that was used by templates that mysteriously disappeared. From what I can tell, system notes are gone when the file is deleted

Are you doing a System Notes saved search?

TLDR - We solved our problem. The prod templates were using URLs to our sandbox file cabinet. We performed a refresh which "deleted" the records in the sandbox causing the broken URLs. I was using a System Notes search. However, when a record is deleted, the system notes pertaining to that record also appear to be deleted. I verified this behavior in sandbox by adding a new file to File cabinet -> view system notes in saved search -> delete file from file cabinet -> observe the system notes are gone.