If you make changes to the content files on your server, you must update the CMS so it knows not to reference these files after you have removed them.

1) In the admin panel navigate to "Utilities" >> batch operations.
Then select sets you wish to batch import should be on the  'include' area. You can use the "Select all" if you want to reindex everything.

select the "Import Content " check box. (no other option can be performed when checking this.
(This will import and index each set's content into the system, but will NOT transcode or create any thumbs. This must be done separately. )

2) When the above import process is finished you will be returned to the Batch Operations page.

Select the sets you wish to reindex again( or select all) and move them to the 'include' area if they are not already selected.

Then select which options you wish to perform on all these sets. Make sure to select the following:

Calculate Image Sizes / Movie Information
Recalculate Set XML
Recalculate Totals

Then scroll down and click "process". Make sure to let the process finish. If you lose internet connection or close this window it will not complete.