After you have moved the directory/project using the context menu > Move directory or Move project, it is displayed at the new position with "A " for "added ".

The command Upload changed files in directories/projects to the server [Upload changed files in directories / projects to the server] changes "A " to a green tick.

The command Check in project (give up editing rights) [Check in project (set read-only)] changes "A " to the lock symbol.