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primary and secondary flight plans

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Why would an FMS need both a primary and secondary flight plan?
Several good reasons. You can copy your Primary FP into the Secondary FP then modify it without the possibility of accidentally screwing up your Primary FP which the FMS is using to navigate.

Why, you might ask, would you want to modify your FP? Good question.
1. Before departure you can delete all the WPs after your initial one then change the destination on the Secondary FP to your departure airport. You can also insert an IAP. If you have an emergency after takeoff just activate the Secondary FP for a quick return.

2. Before departure you can delete all the WPs after your initial one then change the destination on the Secondary FP to your takeoff alternate airport. If you lose one but can't do a quick return due to weather just activate the Secondary FP and proceed to your takeoff alternate.

3. If you arrive in the terminal area when the weather is crappy, fuel is tight and you might have to divert, you can use the Secondary FP to select several different airports to play What If? to see which one might be the most suitable alternate. Once you make the decision to divert just activate the Secondary FP and go.
 
Say you've been cleared direct somewhere, but for some reason, like ATC radar goes down, you have to get back to your flight plan route. Go to the secondary, activate it and clean it up. Much easier than building a new one.
 

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