Since you didn't include any of your code, its somewhat difficult to help diagnose the problem. One of the most common issues with dealing with AS/400 text files is the assumption that text is storeed as ASCII text. All LotusScript statements that write to a file (such as Print #, Put, and Write # ) will convert the characters to the platform-specific code page. The AS/400 platform uses EBCDIC code pages.
The Domino for AS/400 release notes http://doc.notes.net/as400/5.0.7/readas4.nsf/db69c81afd0e71cf852561b700752f5e/fed9cbf1013a6420862569fa007d45b1?OpenDocument&Highlight=0,del,objlnk show how you can use the copy object command to convert the file formats.
Lotus's example: Shell ("CPY OBJ('/acme1/notes/ebcdicfile.txt') TOOBJ('/acme1/notes/asciifile1.txt') FROMCODEPAGE(37) TOCODEPAGE(819)")
You can also use *TEXT and *PCASCII in lieu of 37 ND 819
This was first published in June 2001