This should be fixed in 5.3 according to the roadmap: https://portal.productboard.com/epicgames/1-unreal-engine-public-roadmap/c/1155-nanite
Nanite ISM / Foliage Instance Selection
Several issues in the editor were fixed related to selecting/modifying/deleting instances of Instanced Static Mesh or Foliage Actors that had Nanite enabled.