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How do I apply the mirror modifier properly, I am using the Fuselage as the mirror point, but as soon as I hit apply the flaps get all wonky. what do I need to do to make it work fine?

With modifier:

enter image description here

Applied modifier:

enter image description here

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    $\begingroup$ Don't apply the modifier unless strictly needed. Apply object rotations beforehand, one of the flaps has apparently non zero rotation $\endgroup$ – Duarte Farrajota Ramos Dec 16 '17 at 19:24
  • $\begingroup$ I need to apply the modifier because it is for Flight Simulator. $\endgroup$ – Osian Sodenkamp Dec 16 '17 at 19:51
  • $\begingroup$ I don't think you can apply modifiers on animated geometry like that, unless you somehow manage to convert it to shapekey animations, or use an armature. $\endgroup$ – Duarte Farrajota Ramos Dec 16 '17 at 22:56
  • $\begingroup$ I need to apply the modifiers as when I load the model in Flight Simulator the same result happens. $\endgroup$ – Osian Sodenkamp Dec 17 '17 at 9:12
  • $\begingroup$ you can apply the modifier before you animate but if its already animated go to the dope sheet copy all the keyframes then delete them then apply the modifier then paste the keyframes back $\endgroup$ – The_RedstoneBldr Feb 9 '18 at 23:19
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What do you use for animation? Armature, shape keys, or setting keyframes. Because it really depends on which one you use.

  1. Armature (with bones)

Check out the ORDER of modifiers. If your Armature modifier is below your mirror modifier, switch the order.

  1. shape keys

I doubt you use shape keys because you cannot use mirror modifiers with shape keys. But just in case, check this out. Briefly explained, you can use "mirror shapekeys" at the black triangle below the add-shapekey-button.

  1. setting keyframes

I believe you have nothing set as a mirror object (of mirror modifier). Add an empty and set this as the mirror object.

As for the last solution, I made an example .blend file.

hope it helps

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