This is potentially a good “Idea” you could submit, if nobody provides a known solution.
You can add a warehouse to a part/site, but once transacted against, you can’t delete it. It would be nice to have an “inactive” boolean option to prevent someone from being able to receive/transfer parts to an inactive warehouse (per part).
Are you trying to fix it so this part doesn’t go to this warehouse any longer? The existing inventory is removed from it and placed in the correct warehouse? I am trying to figure out what part of the link you would like to remove. The part could be quantity adjusted out of the wrong warehouse and on the sites area of the part the primary warehouse and primary bins can be changed I believe.
our main manufacturing site has been added as a warehouse to site X
so when site X have zero stock, it still looks like the site has access to all the stock in the manufacturing site - hence no MRP transfer orders autogenerated from MRP