CRTDUPOBJ and LFs will not always work. Speaking from over 14 years in CM on i where CRTDUPOBJ is a common method for putting objects in place on the production server, you JUST CAN'T TRUST IT. I would normally recommend that LFs be the only object type that the source was sent over and the object compiled into place. Had one customer who did NOT have any compiler installed on the production server, yes they had problems.
If you look at the help on CRTDUPOBJ IBM qualifies what will happen with LFs and describes exactly what happened in your case.

When a logical file is copied into another library, two cases
determine the basing for the file:

1. If both the logical file and its based-on physical file are
originally in the same library, a duplicate of the physical
file must be created in the new library before a duplicate of
the logical file is created. After these two duplicates are
created, the new logical file is based on the new physical

2. If the logical file and its based-on physical file are
originally in different libraries, it is not necessary to
duplicate the physical file before duplicating the logical
file. In this case, the duplicated logical file is based on
the same physical file as was the original logical file.
Unlike the first case, even if the physical file is copied
into the new library before the logical file is copied, the
duplicated logical file is based on the original physical
file, not on the duplicated physical file.

I swear the Help used to say you should always check the database relations after using CRTDUPOBJ on a LF...
because you shouldn't trust it.

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