Not sure if this is the same issue, but I had purged a linked block (with nested blocks within that file) and had a similar problem – I could not delete layers or the “ghost” blocks in the block manager. My solution was to 1. make sure all links are current, 2. run purge, 3. save and close file, and finally 4. open the file and run purge again. This deleted all blocks and layers of the links that I couldn’t access/see previously.
These were my reference settings if the image comes through:
