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When a Document is linked to a Task Template, the document is by default allowed to be applied to Standard Tasks created from that Task Template. This is controlled by a Boolean attribute called "To Be Applied to Standard Task" be selected by APM by default. However, in some cases this attribute may be set to False (unselected) for various reasons such as the Task Template and Document link being created in an older version of APM or Ivara EXP, etc. Should the attribute "To Be Applied to Standard Task" be deselected, when clicking on Apply Changes to push Task Template changes from the Template to the Standard Task, the document link may not be pushed to the Standard Task
Open the Task Template to the Properties view > Documents Tab. Update the configuration to include the attribute "To be applied to a standard task". Open each task template and made sure that the "To Be Applied To Standard Tasks" is selected which, sets the Boolean to True. This corrected the problematic task templates but will not expose "Apply changes" method because the change is actually being made to the Document Link not to the Task Template itself. Once the "To Be Applied..." attribute is selected, browse for a new document from the Task Template and link it temporarily then delete the linked new document. The "Apply changes" method will then be exposed.