I don't use the Library update feature on my PSR-800 scanner, which is essentially the same radio as the WS-1080. So what I tell you may not be 100% accurate. But I'll offer some suggestion.
The change that's occurred that you are referring to is not rebanding. The Palmetto 800 system has changed from a scanner TSYS type "MOT 800/900" system to a "P25 AUTO" system type.The system ID and System name have changed. And all of the talkgroup values have changed. From a database perspective, it's (almost) a completely new system.
Library updating requires a few distinct steps. You first download the new library data from the Whistler website to your PC. Then it prompts you to copy the Library data from your PC to your scanner's memory card. Neither of these steps makes any change to your scanner's actual configuration data. The third step it offers you is to update existing configuration items with the updated Library information. I don't know whether this process is "smart" enough to recognize that the Palmetto 800 system is now a new system from a database perspective, and so it may not recognize that new talkgroup values have been added. It may not be able to determine that the trunked system items in your configuration have changed.
You can check all of this yourself by copying the current configuration on your scanner to your PC and analyzing the trunk system types and talkgroups, comparing them to what's listed in the database. You may be required to make some changes manually, or import new data.
Again, I'm not very familiar with how the actual scan data update process works, but my guess it that it's not making all of the changes required in this case.