SVN Error: “‘ ‘x’ isn’t in the same repository as ‘y’ ” during merge

The problem lies in the fact the checkout information is different from what you specify in the svn merge command. Typically, it can be either:

• the hostname is different when you did the checkout. You did the checkout as from svn.example.com but now you are merging by referring to an host alias, like svn-alias.example.com. note that even the case is important. You can get this error if you do svn merge from SVN.EXAMPLE.COM. More on this here and here.
• the protocol is different from what you used for the checkout. E.g. http://svn.example.com versus https://svn.example.com Make sure you use the same protocol.
• you are specifying a username at svn merge in the form [email protected]. Try to remove the user@ specification (the user is passed anyway). svn considers the hostname, and thus the repo, different if you specify the user, even if the user is technically the same.