How can I get old binary files already in CS-RCS to use the new binary archiving mode?

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To change the archiving method of existing binary files, use the Convert form the command-line as follows:
csrcs.exe convert <file name> [-e | -z | -Z] [-d]

-e   Entire File Mode

-z   Zipped Mode

-Z   Zipped Delta Mode

-d   Deep, implement on subfolders. Used with wildcards(*.*) for file name.

Examples:
csrcs convert "C:\ConverterTests\Simple\mypic.bmp" -Z
csrcs convert "C:\ConverterTests\Simple\*.doc" -e
csrcs convert "C:\ConverterTests\Simple\*.*" -z -d

For more details on extension binary modes, refer to Adding a File Type.