Noticed when staging changes from files already in the staged files list. The staged files list lost files (1 out of 7 files) (still appeared in git status from command line). Refreshing via F5 caused the files to reappear immediately, disappear after a second and then reappear permanently a few seconds later thus restoring the view correctly.

The staging view is set to show only Pending, sorted by filename, alphabetic and Flat list multiple columns and Split view staging.

It is unknown what would have happened had I committed if the missing file would have been part of the commit or not.