Mailboxes in your inbox
EFA / EFA Pro / EFA Lite (EFA) normally ignores the inbox and any of its sub-mailboxes when it comes to indexing. However, should you want to file emails into sub-mailboxes of your inbox, then EFA can accommodate this.
In EFA Preferences, go to Exclusions. On the left-hand side, select the INBOX, and if applicable, any mailboxes INBOX/<sub-mailbox> and remove them from the list by clicking on the - button (highlighted in the image with a red box). Close the window, re-start EFA and re-build a full index.