If you have a source containing both a long file name version of a file "THIS_IS_A_TEST_FILE.TXT" and a duplicate 8.3 shorted filename version "THIS_I~1.TXT" the shortened file name will not be copied (even if the shortened filename version does not contain the same data). This problem has to do with how Secure Copy treats files as their shortened names during the copy process it is unable to distinguish between the two seemingly identically named (in 8.3 format) files.
As a workaround create another job with an include files filter of "*~1.*" which will copy only the missing shortened files.
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