Moving a module causes file location in database to be incorrect

Problem/Motivation

Our team manages a lot of Drupal sites which we are upgrading from Drupal 8 to Drupal 9 and we have noticed an issue when modules move their file location. There are a few reasons one might do this:

1. The module goes from being an internal submodule inside a project to being a stand-alone project that is included as a dependency
2. The maintainers of the module have disappeared and you are required to move it into a modules/custom or modules/patched folder.

When you do this, even after running updb and cr and the whole gamut of commands Drupal might start compaining about files being missing from the old folder (whether in /docroot/modules/contrib or even /vendor). This happens throughout the UI and also when running Drush commands.

The usual resolution for this is to:

• Uninstall the module
• Config import to re-install the module and its settings

This is fine for most modules without a database storage component to them, but when you uninstall a module, all the data disappears. You can't use this method to stop the error messages. I have pulled the database and searched through it for references to these files and they are in there, I think mostly in dblog (because of all the errors) and also key_value.

If we were just removing the modules in question, we could use

DELETE FROM key_value WHERE collection='system.schema' AND name='module_name'

but that can't be used here because the module is still in use, just in a different location.

Drupal will often actually find this module, fortunately, and most of the functions will run fine. I have yet to have a critical error come from doing this, but I'm concerned that it's only a matter of time.

Is there a SAFE way to go through and change all the references in the database from the old file location to the new one? Should this not be an automatic process since Drupal is capable of finding modules practically anywhere?