When you drag a file using the book browser Sigil will automatically update the opf to note the change. So, no luck with any kind of automated check of the epubs.
What I do is name the files something that makes sense. Instead of some-long-number.html I would give it:
Code:
cover.html
title.html
epigraph.html
Ch01.html
Ch02.html
...
Ch99.html
AboutheAuthor.html
Alsoby.html
Copyright.html
Then I could easily see if one of the files was out of position.