Updates to collections add new instruments, but deliberately do not replace existing instrument files. In the case of Capsule updates, they also replace the scripting of the patches which also influences legacy patches. In most cases it is best to in existing project replace the old patches with the new ones. If you have made changes to patches (custom CC assingments, Mic position mixes, ...) you can save a Preset in the old patches and import it into the new, transferring all settings.
If you are using BST 2.0 patches with Capsule 2.5, the Modwheel (CC1) will switch between articulation slots in Multi Artic patches. This does not happen when using the 2.1 patches.
To fix this in the 2.0 patches (for example in existing projects) either load the 2.1 patches, or set the "Slot Switch CC" in the Controller Table to another MIDI CC of your choice.
The Slot Switch CC
Our updates by design do not overwrite/delete the old instruments because a lot of users want to keep them. If you do not need older versions anymore, feel free to delete the respective folder(s).