Another tiny little idea…based on something I messed up that was totally my fault, but it gave me the idea at least. 
In file clean-up, remove subfiles option, what about a choice to remove only "orphaned" subfiles—those that are not referenced by ANY other subfile (not just the main one), and that don't themselves reference any other subfiles?
In other words, the same as "All not referenced by main subfile", except that any subfile that references any other subfiles would be treated as a "main" subfile.
The mistake I made was to choose "All not referenced by main subfile", because I had a bunch of little loose subfiles for temporary work that I wanted to quickly delete. But I forgot that there was a major sub-section of my model that wasn't yet referenced by the main subfile, because that doesn't happen until the very final step which I hadn't gotten to yet. So I lost that whole huge chunk of the model along with several subfiles that it contained—and of course I was also silly enough to save the file right after performing the clean-up, but before I realized my mistake!
In file clean-up, remove subfiles option, what about a choice to remove only "orphaned" subfiles—those that are not referenced by ANY other subfile (not just the main one), and that don't themselves reference any other subfiles?
In other words, the same as "All not referenced by main subfile", except that any subfile that references any other subfiles would be treated as a "main" subfile.
The mistake I made was to choose "All not referenced by main subfile", because I had a bunch of little loose subfiles for temporary work that I wanted to quickly delete. But I forgot that there was a major sub-section of my model that wasn't yet referenced by the main subfile, because that doesn't happen until the very final step which I hadn't gotten to yet. So I lost that whole huge chunk of the model along with several subfiles that it contained—and of course I was also silly enough to save the file right after performing the clean-up, but before I realized my mistake!