Perform the following steps to reconfigure repositories and SSH key:
Remove any old SSH keys configured with the Git Integration app via
<JiraHOSTNAME> /secure/ViewSshKeys.jspa(Git Integration for Jira sidebar ➜ SSH keys).
Get the private key file from your Jira server to your Windows workstation:
Open the Connect wizard, use the repository location (git clone URL) and then upload the private key stated above.
For multiple repository configuration, see Bulk change.
More on Working with SSH keys
Reconfigure Git repositories and SSH keys (this page)