You can use the crop feature possibly to crop out a slice of the video that includes the time counter. In the time line you can click on the crop tool in the tool bar at the upper right of your screen and use the Crop to Fill option. Or, you can crop the video to any dimension by selecting it in the media browser (not the timeline) and then clicking on the crop tool and then the crop button above and to the left of the preview screen. You will see adjustment rectangles that allow you to crop to the dimensions that you want. You can use that tool to crop a slice off the bottom of the video while still preserving the aspect ratio and dimensions of the rest of the video.
Another way would be to use the Picture in Picture feature to overlay a small piece of background or blur onto the time counter. That would eliminate the necessity of cropping anything.
-- Rich