IFTHEN is supported in Syncsort 1.3. If it is not working for you, you have done something wrong. What do you mean by "not working" - which is completely worthless to post. You have to post what you tried and what happened.I tried using IF=THEN but the IF=THEN construct itself not working for my SYNSORT. (Please refer my top most post)
For someone here to help, you need to post all of the informational/diagnostic output generated by the run (including the message ids).