If you've authored the complete help in one language, then
copied it and put your localized files in that copy, then you
shouldn't have any missing files or bad links.
If you are adding to your help as development goes on and
you're also delivering to the customer in stages at the same time,
then that adds a bit to the challenge. What I recommend in that
case is whenever you create and finish a new help topic in your
original project, import it into each of your localized copies.
Then the file will be there (untranslated), and links will be
preserved. Then, for example when you get the Spanish version of
the file back, drop it in to the Spanish copy of the help project
so that it saves over the top of the untranslated version.
In this same case, with TOC, glossary, and index files, you
would update the files in the original version of the project. Then
submit the files to be translated. When you get the translated
files back, drop them into the localized projects.
If you're asking for an automatic way to compare, say, an
English project and a Spanish project to make sure all the same
files are in each project, I don't know about that. You may have to
go with some third-party tool to compare file directories. Or go
the good old-fashioned way and eyeball the directories
yourself.