Currently, when you perform a Directory Search, the files are opened using the global default, auto-detect, and fallback encodings. This does not work for a lot of files. For example: Many Shift-JIS files will not be opened with the Shift-JIS encoding even though Shift-JIS is included as a fallback.
When you know the encoding of files to be searched, you should be able to specify that encoding in the search dialog. The only way to do this now is to temporarily change the global default encoding to the search encoding, do any searches, then change it back. The Directory Search dialog should have a configuration field to specify an encoding to use that overrides the global configuration for the duration of that search.