As of Fisheye 4.2 it's possible to rename an existing repository.

Repository name vs key

Each repository has two separate attributes that define its identity.

Name

The name used in the Fisheye UI, including all the dialogs, lists, etc. You define the name when creating a repository, and can change it at any time afterwards (see the section below). The name may contain alphanumeric, underscore, '-' or '.' characters and its length must not exceed 100 characters.

Each defined repository must have a unique name. If another repository with the same name is found when creating or editing a repository, you'll be prompted to change the name to a different value. 

Key

The key is an internal identifier which is included mostly in URLs, REST API, FISHEYE_INST directory, etc. It's set when creating a repository and cannot be changed afterwards.

Each defined repository must have a unique key. When creating a repository, its key is set to a value equal to its name. Potential conflicts are resolved automatically behind-the-scenes: a new repository key is constructed by appending a sequence number to make it unique (e.g. when creating a "foobar" repository its key might be set to "foobar1").

Renaming a repository

To rename a repository

1. Click the 'cog' menu in the Fisheye header, and choose Administration (you'll need to be logged in as an administrator to see this link).
2. Click Repositories (under 'Repository Settings'). 
3. Click the name of the repository (in the 'Name' column). 
4. Click SCM Details in the left menu.
5. Update the Display Name field

 A repository rename operation is performed immediately and doesn't require any subsequent actions such as reindexing.