Netbeans is known to not work correctly with existing local working copies of remote repositories for both SVN and Git. Especially, if they were checked out using client other than built-in into Netbeans. For example, Netbeans does not allows to enter login and password (fields grayed) and thus can't operate on these LWCs.
If you're experiencing such or similar issues, you're highly recommended to delete local working copy and checkout it again, using Netbeans internal client. If you have some changes stashed, you should think about committing and pushing them using different client and then delete LWC and checkout it again.