Broken Configuration Import

Structure:

• Drupal 8 latest, Drush 9
• Local => Dev => Prod structure
• Code managed by composer, git, drush
• Main Dev repo on bitbucket
• Custom profile

Workflow

• We pull the Main Dev Code
• We do development on feature branches on locals and push to main repo
• After review, we merge
• On the Main Dev Server, we fetch, rebase, import configs(drush cim)

Problem
This setup was working perfectly until we noticed the following:

• After attempting to export config (drush cex), we noticed that drush was proposing to delete all the configs in our profile/custom_profile/config/sync; surprising because normally it will create new ones, update modified, and delete removed ones.
• If we approved the deletion, drush will proceed and says all configs where deleted, but the profiles/custom_profile/config/sync still have all the configs, so nothing was deleted.
• When attempting to import new configs, the system acts like it want to create all the configs, like if there is no existing config in the database
• If we approved, we get the following errors:
  1. [warning] array_diff_key(): Argument #1 is not an array ConfigImporter.php:380
  2. Site UUID in source storage does not match the target storage.
  3. Cannot change the install profile from to custom_profile once Drupal is installed. in Drupal\Core\Config\ConfigImporter->validate() (line 737 of /home/devxx/custom_profile/web/core/lib/Drupal/Core/Config/ConfigImporter.php).

No config change is made

Action

• The first action was to delete the newly created configuration and re-attempt config export and import, and everything worked.
• But we need to create new configs; so we checked to make sure there is no mis-configuration, and recreated new config; the export and import still fails with the same error.
• The Site itself works fine; but we cannot import new configs (Create field, content type ...)

More digging

• We checked the config files in profiles/custom_profile/config/sync; there is about 1005 files
• We've noticed that if we have more of that number of files imported, the next import will fail.
• We've attempted to keep last created config that made the import fail, and removed some old fields that where imported when the import was working, to bring the number around 1005 files, and the export and import works.

Current Situation
We are looking in our commits to see if there is no issues with committed UUIDs.
But, IS IT POSSIBLE THAT THERE IS A LIMIT ON THE NUMBER OF CONFIG FILES IN THE DATABASE?
I know this sounds crazy, but I have to ask!