"painstakingly retraced throughout the length" - Yeah, it's not possible to delete ways in the Id editor without following them. Wow.

Features are glued to other features? Then fix it instead of lazily deleting it.

If an alignment of a railtrail dosen't follow the rail ROW, then remove the railway=abandoned there instead of the entire trail.

Don't forget to reply my other comments on your mass deletions and please explain how the traces I pointed out don't actually exist, like you're claiming ("to make sure no trace exists").