I'm trying to replace multiple instances of duplicate parts in an assembly with a single "master" part. Whether I use a macro (ReplaceComponents2) or do it manually via right-click > Replace Components, some components get removed entirely instead of being replaced. They no longer appear in the graphics area, but they still show up in the BOM with the correct quantity.

Has anyone experienced this? Is it a known issue or limitation when replacing multiple components at once? Any workaround to ensure replacements don’t just vanish visually?