The PSoC Programmer 3.13.1 release is a patch update provided support for the advanced release of PSoC Creator 2.0 and still supports PSoC Designer 5.1 SP2 releases.
This release of PSoC Programmer is available through the PSoC Programmer web page and through the CyInstaller Update Manager.
Please navigate to the Programmer Page for the installer and Release Notes.
The new features included with this release includes: update to support the Write Once Latch feature, new PSoC1 CapSense Device Support (CY8C20xx6L), etc.
Boulder, are you referring to a scenario where, you have some data stored in the PSoC's EEPROM and would like to flash the device ? If so, the programming operation will update only the Flash portion. The EEPROM data should be fine.