I've been using the Shadow/Highlight filter for many years without any flicker on 1000's of hours of film transfers that need details lifted out of the crushed shadows and some minor to major highlight recovery. In the timeline, you need to make sure to not have any video on the tracks above or below when using this filter. I do use a title (for masking borders with black rectangles on the left/right sides of the film edges) above the video without issue.
So, for a test, put one video on the timeline and use the Shadow/Highlight filter in Manual mode since Auto will cause flicker. Don't nest anything and put in a new timeline with video above or below as this will probably cause flicker. Also don't make a transition between 2 video clips when using this filter since the clip with this filter applied will flicker.
If you need to stack tracks of video clips then your best option is to export at a high quality format to burn in the filter effect and reimport to put in a timeline with those stacked video clips.
Here is a video example that used the Shadow/Highlight filter: