When an object (a table, a column, a view, or some other object) is invalid within the Query Builder, it will turn red to indicate that an action should be taken to modify or remove it. Hovering over invalid objects presents tooltips with more information on why they are invalid and offer appropriate suggestions for how to resolve issues.
In most cases, red indicates the object was dropped from the server.
Join Lines become red when any of their associated tables, columns, or views are invalid.
If your connection is in an invalid state (if the connection was lost because of a firewall or OS severing idle connections) it's often possible to perform a Reconnect to resolve connection issues. See Reconnecting for more.
Orange backgrounds within Criteria Filter Logic do not indicate an invalid state, orange indicates modifications could be made, but are not required. Hovering over an orange Criteria Filter Logic item produces a tooltip with suggestions for what could be altered.
When [Query] > [Ignore Unused Tables in Diagram] is enabled, any unused tables will be indicated with orange table entity header text. Any unused tables that participate in joins will also change their Join Lines orange and none of their corresponding SQL will appear in the SQL Pane. See Query Options for more on [Ignore Unused Tables in Diagram]