How to ensure database is cataloged
There are 2 types of database directories in Db2 for LUW: system and local.
When you create a database on some path /some_path, the following directory structure is created for this local database directory (if it doesn't exist): /some_path/${DB2INSTANCE}/NODE0000/sqldbdir and the database is cataloged (or registered) in the system database directory automatically.
You may have many local directories in the system, but only one system directory.
You have an ability to uncatalog ("deregister") a database manually afterwards, which removes the corresponding entry from the system directory, but not from the local one. The only way to remove a database from its local directory is to drop it.  

So, the problem described in the doc is about such uncataloged databases, which Db2 instance is unaware of. If you uncataloged your databases previously, and forgot to catalog them again, you should find such databases and catalog them. If you don't remember their local database directory paths, you may use unix find /some_path -type d -name sqldbdir command, and db2 list db directory on /some_path, if you found the directory structure like /some_path/${DB2INSTANCE}/NODE0000/sqldbdir.