I ran into this problem with graphics that I no longer needed in a document. They kept showing up as missing links, with no way to delete them in the Links panel. Apparently, I had Track Changes on, and the deleted graphics were being kept in my tracked changes in the Story Editor. I opened the Track Changes panel (Window > Editorial > Track Changes) then the Story Editor (Edit > Edit In Story Editor). Then in the Track Changes panel, I was able to Accept All Changes > In This Document. This removed all the missing links from the Links panel.