This may be an exercise in futility since the last time I attempted to post in this forum there was nothing I could do that would make it work, so I'm going to keep this really short. Two problems I see are that when you use the filter to replace a section of video with black the marker times are not copied over like they are if you choose to make another filter partial, and that if you have done a number of edits, particularly where you have cut out parts of the video, the make partial option sometimes gets the times wrong, in other words it looks like it transfers what the times would have been if you hadn't made one or more previous edits, so if you don't notice the filter gets applied in the wrong place.
Indeed, with the current design, the selection (the position of markers A and B) can be passed to the partial filter only, and only at creation time. The filter configuration cannot be updated to track later changes to segment layout, so always get the cuts right first, add filters last.