I was able to reproduce this issue on a clean test site with the latest version of Views, so I've escalated it so that it can be sent to the developers for a fix.
Thanks for reporting it, I will update you as soon as I get some feedback.
If you have a slider (which your auto-paginating View effectively is), then when you interact with the View the expectation is that you intend to do something with the currently displayed results.
So if your auto-paginating View has manual pagination controls, for example, as soon as you use one then the auto-pagination stops.
Your use case—where the results of a custom search is output as a slider, and the slider results should update when filters are changed—is a use case that has never come up before and isn't provided for.
He said that he should be able to provide a JS snippet to re-start the auto-pagination after filters have been modified, and when I get that from him I'll pass it on to you.
ok. it's really weird, but I cloned the site using installatron in cpanel, and the new site works - even though the same characters are in the url, it doesn't prevent the slider from working. I don't think I made any changes at all. hidden link
The %5B%5D characters are a red herring, they just confirm that a filter has been specified.
And it is expected that the auto-pagination (which is intended to create sliders) stops when you interact with the View by, for example, setting a filter value.
The developer said that he will take another look at the code he suggested to me to trigger re-starting the pagination when a filter is applied, but suspects it may not be possible after all without some re-writing of how pagination works.
I'm waiting for another update from him to let me know if he has an alternate suggestion, and I'll let you know.
It seems that it is not possible to re-start the auto-pagination after a filter change without some re-factoring of the existing code.
I'm not sure how you seem to have it working, as we've been unable to, and what we see—that auto-pagination stops when the View is interacted with—is the intended result.