As a JIRA admin, I'd like to know how JIRA is dealing with the attachment structure when creating the subfolders inside the attachment directory.

For example:
Let's say that your TEST project has the last issue key TEST-4321.

The directory id created by JIRA will be 10000 until the issue key TEST-10001 is created so JIRA will create the new directory id 20000.

To fix this basically, we'll have to check for each project that has an issue key above 10001 like below:

We found this external article with great informations about this: Handling millions of attachments in JIRA.