Where do you have USERCAT for the ACF2 alternate databases defined? Are they defined in the same USERCAT as the ACF2 primary databases, or are they located on a different USERCAT? Please note that you cannot uncatalog the ACF2 VSAM USERCAT while the ACF2 instance using the corresponding DB is up and running. This will lead to failures.
If you have a separate USERCAT for the ACF2 alternate database, you can issue the switch command, as explained in the techdocs below, to switch to the secondary database and then perform the uncatalog and catalog operation on the primary databases. Once completed, you can switch back to primary.
If the alternate USERCAT exists in the same USERCAT as the primary, you will have to stop ACF2, uncatalog, recatalog, and then restart ACF2.
If the database is shared, the switch or stop of ACF2 will need to be issued on all LPARs sharing the impacted ACF2 DB.
The detailed step-by-step instructions, from taking a backup to switching back to the primary, are explained below. The only change in your case is that instead of deleting and redefining the primary databases, you will just have to uncatalog and catalog the USERCAT volume.