What you need to do is to visit the APM page reached by the "manage files" link on the page brought up for the package. That will show you files that no longer exist (i.e. sql/*.sql files moved to oracle/*.sql and the like). Select the "delete crossed out files" to get rid of them, if any. Then select the "search for new files" and add them - after deleting any junk like "t.tcl" or "temp.xql" etc.
After deleting/adding files take a good look at the list of files and when you're convinced they're all there, THEN write a new .info file.
After writing the .info file commit your changes and, voila, you're done!
