Hi there
Minesh asked me to step in here.
It sounds like you are creating essentially a wireframe of a website—complete with custom post types and fields, views and archives etc.—and distributing that to clients who will then populate it with data.
And your question relates to making changes to the wireframe (maybe adding a form to publish a new post type) and distributing those changes, without affecting the client data, if I understand you correctly.
I don't have a good solution for you that doesn't involve manual intervention, I'm afraid.
We used to have something very similar to what you describe, Toolset Themes, for distributing custom themes alongside Toolset plugins, but it was discontinued due to lack of interest among our client base (and it is not something that can be resurrected).
Which means the only options are, from the source site where you are making changes, to export settings in zip files and import those on the client sites. And this is only a partial solution, because with the advent of blocks this is now only possible for Types and Forms (so not for templates, views, or custom archives), as well as Access settings, if that is relevant.
I wonder if it might be possible to come at this from another direction, whereby you use dedicated import and export tools (such as WP All Import Pro) to export all of the client data, then install an updated wireframe via plugins such as All in One WP Migration (which would reset the client data), then import the client data back in again.
And I don't know if you have considered tools like Appresser that are for distributing WordPress sites as apps. I'm not very familiar with them, but I would imagine they would include the kind of functionality you need.
But as for Toolset itself, it doesn't include the functionality you are asking for, I'm afraid.