Yes, they are certainly there - and I had
backed them
to an external drive in case of mishaps. But I guess that I have a
complete misunderstanding of the whole file system. I imagined
(dreamed) that the OS would live in in its own partition/directory
and could be upgraded without losing access to other software.

What I see is that app's like browsers, email handlers, media players
word processors etc. etc. actually reside with the operating system
and need to be re-installed after the OS installation.