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PDFs are stored on the IFS. Your save procedure should include the SAV command, at least for the directory where the PDFs are located.
For example, to save the entire IFS directories (but not native as400 libraries) you would choose (where tap01 is the tape device name):
SAV DEV('qsys.lib/tap01.devd') OBJ(('/*') ('/QSYS.LIB' *OMIT) ('/QDLS' *OMIT))
Restoring files from the IFS is implemented using the RST command. A good description of the SAV command can be found in this Search400.com tip.
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