SceneMedic targets data duplication and waste. If your file is genuinely full of dense, unique, high-poly meshes and unique 4K textures, that's real content, not bloat — you're looking at a decimation/retopology problem rather than a cleanup one.

No. Downscaling happens in memory only. Your source files on disk are untouched unless you explicitly save the images yourself (Image Editor > Image > Save As). If you save your .blend with packed images, the downscaled versions will be what gets packed.

Instanced objects keep their own location, rotation, scale, and modifiers — only the underlying mesh data is shared. The visible result is identical. Be aware of the trade-off going forward: editing one instanced object in Edit Mode now edits all of them. If you need to edit one separately afterwards, select it and use Object > Relations > Make Single User > Object & Data.

No. Materials are only merged when their node setups are genuinely identical, so the merged result is visually the same material. Anything you customised stays untouched.