There is a BOM command in Eagle (a ULP I think) that automatically generates a BOM. All the metadata associated with a part is saved in the BOM. The BOM will identify what parts (R1, IC1, etc) that the part belongs to, and it can be generated at any time.
Hit the ULP button and look for a ULP file with the word BOM in it, it’s something like MakeBOM or BOM.