There was a time back with QC 9.0 (before 2007) when QC actually DID have an option to store the ''artifacts'' in the DB (as ''blobs'').
This must not have scaled very well as in 9.2, you were REQUIRED to move the repository OUT of the DB and onto the file system (as it is now) before upgrading.

All of your projects were either created much later QC11 + or have been upgraded many times to current, so the DB would not have any repository stuff left over.

That is incorrect.

The REPOSITORY contains ''artifacts'' related to the project:
Test scripts
Test result artifacts - like videos, screenshots
Workflow scripts
Report templates (Word and Excel)
Entity attachments - whatever people attach to defects, tests, etc.

The PROJECT database contains ''transactional'' data as in records created, updated, etc.
It contains pointers to the various artifacts in the repository (like a path).

There is a project-level security (who can do what in the project) stored in the Project DB, and on a higher level (who can see which projects) on the Site Admin (qcsiteadmin_db) database.

If the PROJECT DB is from a totally different time (i.e. months or longer), than the REPOSITORY, we say they are ''out of sync'' and need to be ''re-aligned''.
Re-alignment, relies to reconcile the ''pointers'' from the project DB with the reality in the Repository.
You WILL end up with ''missing'' artifacts, but since either the pointers or artifacts are ''gone'', you can't get to them anyway.