First of all, because uncommitted changes will still cause essentially the same issue in V6R1 as in V5R4, you should use the same procedure regardless of the version/release.
I would create a proc that applied an *EXCLRD lock at the very least on the file before attempting ENDJRNPF. (Actually, I’d more likely apply *EXCL.) If it was a set of files, then I’d apply the lock to each file in the set before going on to journal processing.
The successful establishment of a lock guarantees that you won’t interfere with some other process and that another process won’t interfere with you. Journaling should not be altered while a file is in use.