Are entries ever removed from the Merck Index?
Without several print editions side-by-side, I restrain my answer to the electronic version. This public link or here regarding the online version based on the 14th edition may be read like it may be the case.  To quote:

 "The 14th Edition also contains "retired" records from earlier editions of The Merck Index which still contain valuable information but are no longer being updated with new information."

Of course, beside RSC you may contact them (Merck in Rahway, NJ), too.