Mirror modifier doesn't work (I think)

I’m currently mirroring a right-handed model into a left-handed model.
I used mirror tool as per PLing’s advice. However, I found that the bones were completely messed up when I exported the model.
Later, I found that by using the mirror modifier tool (to flip them), it would revert the bones to the normal arrangements. However, when I exported the model, all changes that I had made with the modifiers had been lost.
What do I do?

And by the way, if anyone has a better idea on how to mirror a model and retain the animations, please post as well.

Bump.

Here’s a useful video to explain it (please read the description).

Did you mirror all of the animations?

The animations were mirrored with the mirror tool.

It seems that everything apart from the modifiers are saved when I export the file.
I tried using collapse stack, but this had no effect; the bones were back in the wrong rotations.