Posted a repro at http://bokand.github.io/bugs/807252/index.html, click anywhere to toggle the bar's position style.

I ran it through a debugger and the change in scroll comes from clamping after layout. There's a bug in layout somewhere, at the time of the clamp, the scrolling box thinks it's clip is the same size as the content, hence the clamp. Afterwards it's correctly sized allowing normal scrolling. This sounds like a bug somewhere in the layout code.

Should mention, this repro'd for me on Linux.

I'm not sure if this is a bug or not, the very same thing happens in Firefox.
If the element has "position: static", it's expected to be painted where it is.

Could you provide screenshots/screencasts or explain better whats the problem?

Could you verify if it works properly in other browsers: Firefox, Edge, Safari?

It works correctly in Firefox. More complete repro steps:

1) Open http://bokand.github.io/bugs/807252/index.html
2) Resize the window so there is vertical scroll extent
3) Scroll down
4) Click anywhere

Expected:
The pink bar disappears, the scroll offset doesn't change

Actual:
The pink bar disappears but the scroll offset is reset to the origin.

Ok, thanks got it now. I'm able to reproduce.
I thought it was related to the position of the element, not about the scroll sorry.
Thanks for the detailed steps.