BizTalk uses a combination of namespace#rootnode to define the schema type of a message, thereby making a MessageType unique (for example http://mynamespace.com#MyRootNode). In other words, BizTalk uses this combination to identify and resolve schemas references.
Then… changing the filename of a schema does not make a new BizTalk schema!!
You could modify the schema namespace or the name of the root node, in order to enable BizTalk to differentiate among the remaining schemas.