Hello,
You have an old version of the S32K reference manual, you can download the newest version available from the following link.
Now regarding the statement. When the condition configured by timer disable (TIMDIS) is detected, the output of the timer will be cleared, it doesn't matter what is the value of the timer, once this condition is detected this output will be cleared automatically. Clearing the output of the timer won't affect the shifters controlled by this timer, this means that the values won't be shifted when this condition occurs unless you generate a shift event with the timer shift clock.
Regards,
Victor