Removed tracks that can no be connected - instruments tracks

Hi, I just updated my orchestral template with the new “Disable Instrument track” option, I moved from rack instruments to track instruments + many midi tracks / multiple outputs.
Every time I open this template I get these popup windows, the midi tracks are routed to the respective disabled track instruments and after enabling it everything works fine, but, Why do I get this popup alerts?, any idea?
Screen Shot 2014-12-23 at 21.57.29.png
Screen Shot 2014-12-23 at 21.57.18.png

I am also getting these and always press cancel to keep my pre-set multiple outputs and groups.

Please SB, some clarifiaction / fix for this.