We didn't change the scrolling logic, which I think was quite broken in master already. At least I know of cases where it didn't work either. This change exposes it much more though.

The smooth auto scrolling (which isn't new functionality) has always had issues like that. It was entirely reworked at some point to address such issues, but without success. Think one of the main problems is that after actions like renaming, it is executed immediately, but the file list is first cleared and then rebuilt. So there is a moment where the scrolling may operate on an empty list, which messes things up.

So I think at this point we should simply remove the smooth auto scrolling, and just ensure the active file is in view bounds after loading using file_ensure_inside_viewbounds(). We can later port this to use UI_view2d_smooth_view(), and make sure that doesn't have conflicts with rebuilding the file list.

I think the problem is the deselection/selection in the code from rB6b0869039a40 [which resorts], not sure if you meant that?
Seems like getting the correct file again after resorting will fix this though, Diff incoming...

There might be situations where there is an empty list (havent run into this though I think), but the clear regression from the culprit commit should still be fixed?