How to handle filtering on table columns?

I am currently working on a pretty complex (and convoluted, I'll admit) table in terms of filtering. One of the options for filtering allows the user to filter on an item that is displayed as a column and I'm trying to figure out the least confusing / jarring way to update the table for it.

This is hard to describe in words, I'll be honest so here's a GIF showing the functionality.

I added blocks to hide some data so pay no mind to the floating grey boxes :).

Currently, only the selected items for that filter are shown in the table and the rest are removed. This has the benefits that the user doesn't have to see or think about information that they don't care about, but then they have to re-adjust to what is effectively a "new" table. The other option is to gray out the unselected columns so the information is still there but taken out of focus.

What method from the above, or some other if you have ideas, do you think would confuse the user the least?