MHA never amended the Civil Defence Act, 1968 to remove Sikkim's reference. Attaching the last amendment done in 2009, which did not touch the issue. The Act is there on https://dgfscdhg.gov.in/civil-defence 
Delhi govt babu simply reproduced what is there in MHA records,y suspend him? https://twitter.com/rammadhavbjp/status/1264191269409972225

This is from Assam government's website. The objectionable reference to Sikkim also mentioned here.
MHA should amend the 1968 Act first!

An MHA official has clarified that a separate amendment is not required, and the parent Act should have been read with the footnote (attached below). No clarity on mention of the same Sikkim reference on websites of other State governments such as Assam and U.P.