How Can I Update Content Types / Lists / Groups / Users in an Office Dev PnP Provisioning Template

In Provisioning Templates some updates (especially additions but some configuration changes also) will just be applied if you modify the template and apply it again to the same site.

Removal of elements and lots of other configuration changes are not (yet) implemented in the engine but in general you could easily write some code using one of the extension methods in the Core library to do so if needed. You could hook this code up to your provisioning template by defining Extensiblity Handlers or you could execute this kind of code wherever makes sense.

Hope this helps!