Thermal paste residue very difficult to clean
Cleaner is always better for thermal contact. I'd try scraping with a razor blade and then removing any remaining residue with a stronger solvent like acetone. You can also use very fine sandpaper, like 600 grit, to abrade and clean the surface. You want a very flat, clean surface, so that the new thermal paste is filling only the tiniest gap between the GPU and the heat sink, because the thermal paste is far less conductive of heat than copper or aluminum, so less thermal paste is better.