We don't recommend removing the source files after your transcoding jobs are finished, but if you do, you need to do a few steps in order to maintain the integrity of the CMS file index.
1) After you delete the source files from the server(usually inside the 'source' subfolder of your set folders, you need to run a batch to update the system using the batch tool(Utilities >> Batch Operations) to 'Import content' to re-scan all the sets you have removed the source files for. In the Batch tool, select all the sets in which you have removed the source files, then move them to the right-hand side include list. Then select the checkbox for
"Import Content "
(when you do this all other options will be grayed out.) Then scroll down and select "Process".
2) When this operation is finished, do the same operations above to select the sets and move to the right-hand side, but instead of choosing "Import Content", select the following options:
Calculate Image Sizes / Movie Information ( vids )
Recalculate Set XML ( ? ) Help
Recalculate Content Totals
Then scroll down and click "Process" again.
What this does is remove any references to the source files so in the future when you try to make a thumbnail, edit a date, or some other function, the system doesn't error out when it can't find the file you removed.